rs10012953

Variant names:

• chr4-110043206-A-G
• rs10012953

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 0.215 in 152,170 control chromosomes in the GnomAD database, including 3,701 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 0.21 (3701 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.42
• Publications: 13 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.49).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.235 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: 0.215 AC: 32699 AN: 152052 Hom.: 3700 Cov.: 31

Gnomad AFR AF: 0.181

Gnomad AMI AF: 0.143

Gnomad AMR AF: 0.206

Gnomad ASJ AF: 0.289

Gnomad EAS AF: 0.121

Gnomad SAS AF: 0.152

Gnomad FIN AF: 0.262

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.238

Gnomad OTH AF: 0.224

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

GnomAD4 genome AF: 0.215 AC: 32697 AN: 152170 Hom.: 3701 Cov.: 31 AF XY: 0.214 AC XY: 15903 AN XY: 74398

African (AFR) AF: 0.181 AC: 7502 AN: 41512

American (AMR) AF: 0.206 AC: 3147 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.289 AC: 1003 AN: 3466

East Asian (EAS) AF: 0.122 AC: 629 AN: 5176

South Asian (SAS) AF: 0.151 AC: 730 AN: 4824

European-Finnish (FIN) AF: 0.262 AC: 2774 AN: 10574

Middle Eastern (MID) AF: 0.333 AC: 98 AN: 294

European-Non Finnish (NFE) AF: 0.238 AC: 16216 AN: 68006

Other (OTH) AF: 0.222 AC: 468 AN: 2108

Alfa AF: 0.229 Hom.: 9126

Bravo AF: 0.210

Asia WGS AF: 0.141 AC: 490 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.49
CADD	Benign	15
DANN	Benign	0.77
PhyloP100		2.4

Splicing

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

Other links and lift over

dbSNP: rs10012953; hg19: chr4-110964362;