chr1-158382610-T-G

Variant names:

• chr1-158382610-T-G
• rs11264965

Variant summary

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

The variant allele was found at a frequency of 0.355 in 151,690 control chromosomes in the GnomAD database, including 11,864 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 0.36 (11864 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.29
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.624 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

Frequencies

GnomAD3 genomes AF: 0.355 AC: 53754 AN: 151572 Hom.: 11822 Cov.: 32

Gnomad AFR AF: 0.630

Gnomad AMI AF: 0.304

Gnomad AMR AF: 0.287

Gnomad ASJ AF: 0.261

Gnomad EAS AF: 0.266

Gnomad SAS AF: 0.318

Gnomad FIN AF: 0.290

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.229

Gnomad OTH AF: 0.304

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

GnomAD4 genome AF: 0.355 AC: 53860 AN: 151690 Hom.: 11864 Cov.: 32 AF XY: 0.355 AC XY: 26340 AN XY: 74144

African (AFR) AF: 0.631 AC: 26105 AN: 41380

American (AMR) AF: 0.287 AC: 4361 AN: 15202

Ashkenazi Jewish (ASJ) AF: 0.261 AC: 905 AN: 3466

East Asian (EAS) AF: 0.265 AC: 1367 AN: 5152

South Asian (SAS) AF: 0.318 AC: 1530 AN: 4812

European-Finnish (FIN) AF: 0.290 AC: 3065 AN: 10578

Middle Eastern (MID) AF: 0.228 AC: 67 AN: 294

European-Non Finnish (NFE) AF: 0.229 AC: 15538 AN: 67792

Other (OTH) AF: 0.307 AC: 645 AN: 2104

Alfa AF: 0.226 Hom.: 1080

Bravo AF: 0.362

Asia WGS AF: 0.339 AC: 1178 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.45
DANN	Benign	0.58
PhyloP100		-2.3

Splicing

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

Other links and lift over

dbSNP: rs11264965; hg19: chr1-158352400;