rs313909

Variant names:

• chr16-2287992-G-A
• rs313909
• NM_001089.3:c.3004+34C>T

Your query was ambiguous. Multiple possible variants found:

• chr16-2287992-G-A
• chr16-2287992-G-C
• chr16-2287992-G-T

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_001089.3(ABCA3):​c.3004+34C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.409 in 1,594,848 control chromosomes in the GnomAD database, including 135,182 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.43 (14400 hom., cov: 32)
  • Exomes 𝑓: 0.41 (120782 hom.)
• Consequence: ABCA3 NM_001089.3 intron
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -0.142

Genes affected

ABCA3 (HGNC:33): (ATP binding cassette subfamily A member 3) The membrane-associated protein encoded by this gene is a member of the superfamily of ATP-binding cassette (ABC) transporters. ABC proteins transport various molecules across extra- and intracellular membranes. ABC genes are divided into seven distinct subfamilies (ABC1, MDR/TAP, MRP, ALD, OABP, GCN20, White). This protein is a member of the ABC1 subfamily. Members of the ABC1 subfamily comprise the only major ABC subfamily found exclusively in multicellular eukaryotes. The full transporter encoded by this gene may be involved in development of resistance to xenobiotics and engulfment during programmed cell death. [provided by RefSeq, Jul 2008]

ACMG classification

Our verdict: Benign. The variant received -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BP6: Variant 16-2287992-G-A is Benign according to our data. Variant chr16-2287992-G-A is described in ClinVar as [Benign]. Clinvar id is 1290757.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.488 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ABCA3	NM_001089.3	c.3004+34C>T		intron_variant	Intron 21 of 32	ENST00000301732.10	NP_001080.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ABCA3	ENST00000301732.10	c.3004+34C>T		intron_variant	Intron 21 of 32	1	NM_001089.3	ENSP00000301732.5
ABCA3	ENST00000382381.7	c.2830+34C>T		intron_variant	Intron 20 of 31	1		ENSP00000371818.3

Frequencies

GnomAD3 genomes AF: 0.432 AC: 65649 AN: 151948 Hom.: 14391 Cov.: 32

Gnomad AFR AF: 0.494

Gnomad AMI AF: 0.512

Gnomad AMR AF: 0.385

Gnomad ASJ AF: 0.461

Gnomad EAS AF: 0.452

Gnomad SAS AF: 0.505

Gnomad FIN AF: 0.393

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.402

Gnomad OTH AF: 0.415

GnomAD2 exomes AF: 0.415 AC: 95750 AN: 230630 AF XY: 0.420

Gnomad AFR exome AF: 0.502

Gnomad AMR exome AF: 0.356

Gnomad ASJ exome AF: 0.453

Gnomad EAS exome AF: 0.447

Gnomad FIN exome AF: 0.396

Gnomad NFE exome AF: 0.394

Gnomad OTH exome AF: 0.409

GnomAD4 exome AF: 0.407 AC: 586657 AN: 1442784 Hom.: 120782 Cov.: 39 AF XY: 0.410 AC XY: 294231 AN XY: 717762

Gnomad4 AFR exome AF: 0.503 AC: 16783 AN: 33362

Gnomad4 AMR exome AF: 0.359 AC: 16019 AN: 44578

Gnomad4 ASJ exome AF: 0.452 AC: 11801 AN: 26088

Gnomad4 EAS exome AF: 0.444 AC: 17583 AN: 39628

Gnomad4 SAS exome AF: 0.496 AC: 42690 AN: 86034

Gnomad4 FIN exome AF: 0.395 AC: 15476 AN: 39208

Gnomad4 NFE exome AF: 0.396 AC: 438968 AN: 1109628

Gnomad4 Remaining exome AF: 0.423 AC: 25384 AN: 59962

GnomAD4 genome AF: 0.432 AC: 65685 AN: 152064 Hom.: 14400 Cov.: 32 AF XY: 0.431 AC XY: 32035 AN XY: 74324

Gnomad4 AFR AF: 0.493 AC: 0.493347 AN: 0.493347

Gnomad4 AMR AF: 0.384 AC: 0.384182 AN: 0.384182

Gnomad4 ASJ AF: 0.461 AC: 0.460829 AN: 0.460829

Gnomad4 EAS AF: 0.452 AC: 0.45215 AN: 0.45215

Gnomad4 SAS AF: 0.505 AC: 0.504562 AN: 0.504562

Gnomad4 FIN AF: 0.393 AC: 0.392938 AN: 0.392938

Gnomad4 NFE AF: 0.402 AC: 0.402322 AN: 0.402322

Gnomad4 OTH AF: 0.419 AC: 0.418638 AN: 0.418638

Alfa AF: 0.370 Hom.: 2762

Bravo AF: 0.430

Asia WGS AF: 0.502 AC: 1745 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

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Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Jul 21, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.3
DANN	Benign	0.47
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs313909; hg19: chr16-2337993;