rs10195265

Variant names:

• chr2-146078690-A-C
• rs10195265
• ENST00000790596.1:n.115+10979T>G

Variant summary

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

The ENST00000790596.1(ENSG00000302944):​n.115+10979T>G variant causes a intron change. The variant allele was found at a frequency of 0.0247 in 152,004 control chromosomes in the GnomAD database, including 127 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 0.025 (127 hom., cov: 32)
• Consequence: ENSG00000302944 ENST00000790596.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.96
• Publications: 2 publications found

Genes affected

ENSG00000302944 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.47).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0867 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
ENSG00000302944	ENST00000790596.1	n.115+10979T>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0246 AC: 3732 AN: 151884 Hom.: 127 Cov.: 32

Gnomad AFR AF: 0.00519

Gnomad AMI AF: 0.0736

Gnomad AMR AF: 0.0875

Gnomad ASJ AF: 0.00490

Gnomad EAS AF: 0.0320

Gnomad SAS AF: 0.0936

Gnomad FIN AF: 0.0220

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0174

Gnomad OTH AF: 0.0273

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

GnomAD4 genome AF: 0.0247 AC: 3747 AN: 152004 Hom.: 127 Cov.: 32 AF XY: 0.0268 AC XY: 1996 AN XY: 74350

African (AFR) AF: 0.00520 AC: 216 AN: 41528

American (AMR) AF: 0.0878 AC: 1337 AN: 15220

Ashkenazi Jewish (ASJ) AF: 0.00490 AC: 17 AN: 3466

East Asian (EAS) AF: 0.0319 AC: 165 AN: 5172

South Asian (SAS) AF: 0.0939 AC: 453 AN: 4826

European-Finnish (FIN) AF: 0.0220 AC: 233 AN: 10612

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.0174 AC: 1183 AN: 67868

Other (OTH) AF: 0.0304 AC: 64 AN: 2108

Alfa AF: 0.0172 Hom.: 4

Bravo AF: 0.0284

Asia WGS AF: 0.0740 AC: 256 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.47
CADD	Benign	16
DANN	Benign	0.54
PhyloP100		4.0

Splicing

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

Other links and lift over

dbSNP: rs10195265; hg19: chr2-146836258;