rs2634685

Variant names:

• chr12-48374772-G-A
• rs2634685
• ENST00000548257.1:n.237+17180G>A

Your query was ambiguous. Multiple possible variants found:

• chr12-48374772-G-A
• chr12-48374772-G-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000548257.1(ENSG00000257735):​n.237+17180G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.555 in 151,946 control chromosomes in the GnomAD database, including 27,099 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 0.55 (27099 hom., cov: 31)
• Consequence: ENSG00000257735 ENST00000548257.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.513
• Publications: 10 publications found

Genes affected

ENSG00000257735 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.733 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000257735	ENST00000548257.1	n.237+17180G>A		intron_variant	Intron 3 of 3	4
ENSG00000293682	ENST00000717861.1	n.451+17180G>A		intron_variant	Intron 4 of 4
ENSG00000257735	ENST00000717862.1	n.401-38649G>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.555 AC: 84255 AN: 151826 Hom.: 27090 Cov.: 31

Gnomad AFR AF: 0.245

Gnomad AMI AF: 0.775

Gnomad AMR AF: 0.527

Gnomad ASJ AF: 0.739

Gnomad EAS AF: 0.232

Gnomad SAS AF: 0.584

Gnomad FIN AF: 0.682

Gnomad MID AF: 0.731

Gnomad NFE AF: 0.738

Gnomad OTH AF: 0.606

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

GnomAD4 genome AF: 0.555 AC: 84292 AN: 151946 Hom.: 27099 Cov.: 31 AF XY: 0.551 AC XY: 40937 AN XY: 74276

African (AFR) AF: 0.245 AC: 10161 AN: 41440

American (AMR) AF: 0.527 AC: 8037 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.739 AC: 2565 AN: 3470

East Asian (EAS) AF: 0.233 AC: 1202 AN: 5168

South Asian (SAS) AF: 0.585 AC: 2813 AN: 4808

European-Finnish (FIN) AF: 0.682 AC: 7198 AN: 10560

Middle Eastern (MID) AF: 0.724 AC: 210 AN: 290

European-Non Finnish (NFE) AF: 0.738 AC: 50137 AN: 67934

Other (OTH) AF: 0.600 AC: 1262 AN: 2104

Alfa AF: 0.673 Hom.: 114749

Bravo AF: 0.528

Asia WGS AF: 0.408 AC: 1424 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	6.8
DANN	Benign	0.85
PhyloP100		-0.51

Splicing

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

Other links and lift over

dbSNP: rs2634685; hg19: chr12-48768555;