rs13014982

Variant names:

• chr2-163470244-G-A
• rs13014982
• ENST00000809663.1:n.377-4764G>A

Variant summary

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

The ENST00000809663.1(ENSG00000305215):​n.377-4764G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.321 in 150,508 control chromosomes in the GnomAD database, including 8,101 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 0.32 (8101 hom., cov: 31)
• Consequence: ENSG00000305215 ENST00000809663.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.241
• Publications: 4 publications found

Genes affected

ENSG00000305215 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.406 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000809663.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000305215	ENST00000809663.1		n.377-4764G>A		intron	N/A
	ENSG00000305215	ENST00000809664.1		n.376-4764G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.321 AC: 48230 AN: 150400 Hom.: 8100 Cov.: 31

Gnomad AFR AF: 0.206

Gnomad AMI AF: 0.440

Gnomad AMR AF: 0.414

Gnomad ASJ AF: 0.469

Gnomad EAS AF: 0.394

Gnomad SAS AF: 0.224

Gnomad FIN AF: 0.361

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.352

Gnomad OTH AF: 0.352

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

GnomAD4 genome AF: 0.321 AC: 48260 AN: 150508 Hom.: 8101 Cov.: 31 AF XY: 0.322 AC XY: 23666 AN XY: 73464

African (AFR) AF: 0.207 AC: 8361 AN: 40442

American (AMR) AF: 0.415 AC: 6287 AN: 15164

Ashkenazi Jewish (ASJ) AF: 0.469 AC: 1623 AN: 3462

East Asian (EAS) AF: 0.394 AC: 2015 AN: 5108

South Asian (SAS) AF: 0.225 AC: 1075 AN: 4788

European-Finnish (FIN) AF: 0.361 AC: 3748 AN: 10392

Middle Eastern (MID) AF: 0.514 AC: 150 AN: 292

European-Non Finnish (NFE) AF: 0.352 AC: 23870 AN: 67862

Other (OTH) AF: 0.350 AC: 730 AN: 2086

Alfa AF: 0.350 Hom.: 1517

Bravo AF: 0.323

Asia WGS AF: 0.262 AC: 911 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.74
DANN	Benign	0.45
PhyloP100		0.24

Splicing

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

Other links and lift over

dbSNP: rs13014982; hg19: chr2-164326754;