rs2991396

Variant names:

• chr13-67315254-G-A
• rs2991396
• XR_002957498.1:n.131+4485C>T

Your query was ambiguous. Multiple possible variants found:

• chr13-67315254-G-A
• chr13-67315254-G-C
• chr13-67315254-G-T

Variant summary

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

The XR_942037.1(LOC105370246):​n.131+4485C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.713 in 151,870 control chromosomes in the GnomAD database, including 39,434 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 0.71 (39434 hom., cov: 31)
• Consequence: LOC105370246 XR_942037.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.312
• Publications: 3 publications found

Genes affected

LOC105370246 (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 (EAS) allele frequency at 95% confidence interval = 0.893 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.714 AC: 108277 AN: 151750 Hom.: 39421 Cov.: 31

Gnomad AFR AF: 0.561

Gnomad AMI AF: 0.826

Gnomad AMR AF: 0.697

Gnomad ASJ AF: 0.768

Gnomad EAS AF: 0.914

Gnomad SAS AF: 0.726

Gnomad FIN AF: 0.810

Gnomad MID AF: 0.736

Gnomad NFE AF: 0.775

Gnomad OTH AF: 0.696

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

GnomAD4 genome AF: 0.713 AC: 108338 AN: 151870 Hom.: 39434 Cov.: 31 AF XY: 0.715 AC XY: 53057 AN XY: 74234

African (AFR) AF: 0.560 AC: 23190 AN: 41392

American (AMR) AF: 0.697 AC: 10608 AN: 15216

Ashkenazi Jewish (ASJ) AF: 0.768 AC: 2665 AN: 3468

East Asian (EAS) AF: 0.915 AC: 4728 AN: 5166

South Asian (SAS) AF: 0.725 AC: 3489 AN: 4810

European-Finnish (FIN) AF: 0.810 AC: 8566 AN: 10570

Middle Eastern (MID) AF: 0.738 AC: 217 AN: 294

European-Non Finnish (NFE) AF: 0.775 AC: 52649 AN: 67938

Other (OTH) AF: 0.700 AC: 1474 AN: 2106

Alfa AF: 0.753 Hom.: 81654

Bravo AF: 0.702

Asia WGS AF: 0.801 AC: 2789 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.3
DANN	Benign	0.41
PhyloP100		0.31

Splicing

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

Other links and lift over

dbSNP: rs2991396; hg19: chr13-67889386; COSMIC: COSV69359908;