17-50660500-C-G

Variant names:

• chr17-50660500-C-G
• rs1978153
• NM_003786.4:c.807-423C>G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_003786.4(ABCC3):​c.807-423C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.416 in 151,954 control chromosomes in the GnomAD database, including 13,276 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.42 (13276 hom., cov: 31)
• Consequence: ABCC3 NM_003786.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.659

Genes affected

ABCC3 (HGNC:54): (ATP binding cassette subfamily C member 3) 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). This protein is a member of the MRP subfamily which is involved in multi-drug resistance. The specific function of this protein has not yet been determined; however, this protein may play a role in the transport of biliary and intestinal excretion of organic anions. Alternatively spliced variants which encode different protein isoforms have been described; however, not all variants have been fully characterized. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.529 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ABCC3	NM_003786.4	c.807-423C>G		intron_variant	Intron 7 of 30	ENST00000285238.13	NP_003777.2
ABCC3	NM_001144070.2	c.807-423C>G		intron_variant	Intron 7 of 11		NP_001137542.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ABCC3	ENST00000285238.13	c.807-423C>G		intron_variant	Intron 7 of 30	1	NM_003786.4	ENSP00000285238.8

Frequencies

GnomAD3 genomes AF: 0.416 AC: 63183 AN: 151834 Hom.: 13275 Cov.: 31

Gnomad AFR AF: 0.417

Gnomad AMI AF: 0.434

Gnomad AMR AF: 0.367

Gnomad ASJ AF: 0.458

Gnomad EAS AF: 0.391

Gnomad SAS AF: 0.547

Gnomad FIN AF: 0.483

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.406

Gnomad OTH AF: 0.419

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.416 AC: 63200 AN: 151954 Hom.: 13276 Cov.: 31 AF XY: 0.421 AC XY: 31236 AN XY: 74250

Gnomad4 AFR AF: 0.417

Gnomad4 AMR AF: 0.367

Gnomad4 ASJ AF: 0.458

Gnomad4 EAS AF: 0.390

Gnomad4 SAS AF: 0.547

Gnomad4 FIN AF: 0.483

Gnomad4 NFE AF: 0.406

Gnomad4 OTH AF: 0.417

Alfa AF: 0.303 Hom.: 915

Bravo AF: 0.407

Asia WGS AF: 0.491 AC: 1712 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.2
DANN	Benign	0.75

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: rs1978153; hg19: chr17-48737861;