rs10158916

Variant names:

• chr1-79707927-A-G
• rs10158916

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 0.0755 in 151,922 control chromosomes in the GnomAD database, including 930 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 0.076 (930 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.379
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.257 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: 0.0753 AC: 11429 AN: 151804 Hom.: 920 Cov.: 32

Gnomad AFR AF: 0.180

Gnomad AMI AF: 0.0274

Gnomad AMR AF: 0.0507

Gnomad ASJ AF: 0.00318

Gnomad EAS AF: 0.268

Gnomad SAS AF: 0.0670

Gnomad FIN AF: 0.0409

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0129

Gnomad OTH AF: 0.0645

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

GnomAD4 genome AF: 0.0755 AC: 11477 AN: 151922 Hom.: 930 Cov.: 32 AF XY: 0.0770 AC XY: 5714 AN XY: 74238

African (AFR) AF: 0.181 AC: 7486 AN: 41470

American (AMR) AF: 0.0508 AC: 774 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.00318 AC: 11 AN: 3460

East Asian (EAS) AF: 0.269 AC: 1393 AN: 5174

South Asian (SAS) AF: 0.0672 AC: 324 AN: 4818

European-Finnish (FIN) AF: 0.0409 AC: 433 AN: 10580

Middle Eastern (MID) AF: 0.0170 AC: 5 AN: 294

European-Non Finnish (NFE) AF: 0.0129 AC: 878 AN: 67852

Other (OTH) AF: 0.0700 AC: 148 AN: 2114

Alfa AF: 0.0537 Hom.: 79

Bravo AF: 0.0807

Asia WGS AF: 0.178 AC: 617 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	3.6
DANN	Benign	0.74
PhyloP100		-0.38

Splicing

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

Other links and lift over

dbSNP: rs10158916; hg19: chr1-80173612;