17-50634975-G-A

Variant names:

• chr17-50634975-G-A
• rs201886646
• NM_003786.4:c.39G>A

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_003786.4(ABCC3):​c.39G>A​(p.Lys13Lys) variant causes a synonymous change. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 34)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: ABCC3 NM_003786.4 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.75
• Publications: 8 publications found

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]

ENSG00000251239 (HGNC:):

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.32).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_003786.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ABCC3	NM_003786.4	MANE Select	c.39G>A	p.Lys13Lys	synonymous	Exon 1 of 31	NP_003777.2
	ABCC3	NM_001144070.2		c.39G>A	p.Lys13Lys	synonymous	Exon 1 of 12	NP_001137542.1	O15438-5

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ABCC3	ENST00000285238.13	TSL:1 MANE Select	c.39G>A	p.Lys13Lys	synonymous	Exon 1 of 31	ENSP00000285238.8	O15438-1
	ABCC3	ENST00000427699.5	TSL:1	c.39G>A	p.Lys13Lys	synonymous	Exon 1 of 12	ENSP00000395160.1	O15438-5
	ABCC3	ENST00000871907.1		c.39G>A	p.Lys13Lys	synonymous	Exon 1 of 31	ENSP00000541966.1

Frequencies

GnomAD3 genomes Cov.: 34

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 1108008 Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0 AN XY: 526206

African (AFR) AF: 0.00 AC: 0 AN: 23708

American (AMR) AF: 0.00 AC: 0 AN: 9396

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 14538

East Asian (EAS) AF: 0.00 AC: 0 AN: 27540

South Asian (SAS) AF: 0.00 AC: 0 AN: 23920

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 29106

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 3008

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 932370

Other (OTH) AF: 0.00 AC: 0 AN: 44422

GnomAD4 genome Cov.: 34

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.32
CADD	Benign	15
DANN	Uncertain	0.98
PhyloP100		3.7
PromoterAI		0.0058	Neutral
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		2.5

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

Other links and lift over

dbSNP: rs201886646; hg19: chr17-48712336;