rs10914952

Variant names:

• chr1-34453612-G-A
• rs10914952

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 0.218 in 152,072 control chromosomes in the GnomAD database, including 3,775 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 0.22 (3775 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.832
• Publications: 0 publications found

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 = 0.278 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: 0.218 AC: 33182 AN: 151952 Hom.: 3773 Cov.: 32

Gnomad AFR AF: 0.242

Gnomad AMI AF: 0.124

Gnomad AMR AF: 0.261

Gnomad ASJ AF: 0.170

Gnomad EAS AF: 0.289

Gnomad SAS AF: 0.267

Gnomad FIN AF: 0.153

Gnomad MID AF: 0.229

Gnomad NFE AF: 0.199

Gnomad OTH AF: 0.240

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

GnomAD4 genome AF: 0.218 AC: 33210 AN: 152072 Hom.: 3775 Cov.: 32 AF XY: 0.221 AC XY: 16453 AN XY: 74360

African (AFR) AF: 0.242 AC: 10044 AN: 41456

American (AMR) AF: 0.261 AC: 3990 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.170 AC: 590 AN: 3470

East Asian (EAS) AF: 0.290 AC: 1497 AN: 5164

South Asian (SAS) AF: 0.267 AC: 1283 AN: 4800

European-Finnish (FIN) AF: 0.153 AC: 1619 AN: 10600

Middle Eastern (MID) AF: 0.231 AC: 68 AN: 294

European-Non Finnish (NFE) AF: 0.199 AC: 13504 AN: 67986

Other (OTH) AF: 0.238 AC: 502 AN: 2108

Alfa AF: 0.205 Hom.: 4843

Bravo AF: 0.227

Asia WGS AF: 0.248 AC: 861 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	5.8
DANN	Benign	0.56
PhyloP100		0.83

Splicing

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

Other links and lift over

dbSNP: rs10914952; hg19: chr1-34919213;