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_002957498.1(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_002957498.1 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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105370246	XR_002957498.1	n.131+4485C>T		intron_variant	Intron 2 of 2
LOC105370246	XR_942037.1	n.131+4485C>T		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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 v4.3

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;