rs2239320

Positions:

• chr16-16212071-A-G
• chr16-16212071-A-T

Variant summary

Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4_Strong BP6

The NM_001171.6(ABCC6):​c.662+114T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in Lovd as Benign (no stars).

• Frequency:
  • Genomes: 𝑓 0.043 (198 hom., cov: 22)
  • Exomes 𝑓: 0.00022 (11 hom.)
  • Failed GnomAD Quality Control
• Consequence: ABCC6 NM_001171.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.952

Genes affected

ABCC6 (HGNC:57): (ATP binding cassette subfamily C member 6) The 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 intra-cellular membranes. ABC genes are divided into seven distinct subfamilies (ABC1, MDR/TAP, MRP, ALD, OABP, GCN20, White). The encoded protein, a member of the MRP subfamily, is involved in multi-drug resistance. Mutations in this gene cause pseudoxanthoma elasticum. Alternatively spliced transcript variants that encode different proteins have been described for this gene. [provided by RefSeq, Jul 2008]

LOC105371100 (HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -5 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BP6: Variant 16-16212071-A-G is Benign according to our data. Variant chr16-16212071-A-G is described in Lovd as [Benign].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ABCC6	NM_001171.6	c.662+114T>C		intron_variant		ENST00000205557.12	NP_001162.5
LOC105371100	XR_933131.3	n.262A>G		non_coding_transcript_exon_variant	2/3
ABCC6	NM_001351800.1	c.320+114T>C		intron_variant			NP_001338729.1
ABCC6	NR_147784.1	n.699+114T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ABCC6	ENST00000205557.12	c.662+114T>C		intron_variant		1	NM_001171.6	ENSP00000205557	P1

Frequencies

GnomAD3 genomes AF: 0.00 AC: 4179 AN: 97134 Hom.: 197 Cov.: 22 FAILED QC

Gnomad AFR AF: 0.0790

Gnomad AMI AF: 0.0464

Gnomad AMR AF: 0.0359

Gnomad ASJ AF: 0.0447

Gnomad EAS AF: 0.103

Gnomad SAS AF: 0.0478

Gnomad FIN AF: 0.0129

Gnomad MID AF: 0.0607

Gnomad NFE AF: 0.0325

Gnomad OTH AF: 0.0581

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.000224 AC: 138 AN: 615652 Hom.: 11 AF XY: 0.000244 AC XY: 80 AN XY: 327512

Gnomad4 AFR exome AF: 0.000777

Gnomad4 AMR exome AF: 0.000200

Gnomad4 ASJ exome AF: 0.000112

Gnomad4 EAS exome AF: 0.000868

Gnomad4 SAS exome AF: 0.000130

Gnomad4 FIN exome AF: 0.000104

Gnomad4 NFE exome AF: 0.000195

Gnomad4 OTH exome AF: 0.000267

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.0430 AC: 4175 AN: 97158 Hom.: 198 Cov.: 22 AF XY: 0.0396 AC XY: 1897 AN XY: 47860

Gnomad4 AFR AF: 0.0789

Gnomad4 AMR AF: 0.0357

Gnomad4 ASJ AF: 0.0447

Gnomad4 EAS AF: 0.103

Gnomad4 SAS AF: 0.0482

Gnomad4 FIN AF: 0.0129

Gnomad4 NFE AF: 0.0325

Gnomad4 OTH AF: 0.0576

Alfa AF: 0.232 Hom.: 744

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.2
DANN	Benign	0.73

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: rs2239320; hg19: chr16-16305928;