10-53722881-A-G

Variant names:

• chr10-53722881-A-G
• rs10508997

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 0.2 in 152,000 control chromosomes in the GnomAD database, including 4,253 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 0.20 (4253 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.230
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.654 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: 0.200 AC: 30413 AN: 151882 Hom.: 4243 Cov.: 32

Gnomad AFR AF: 0.0579

Gnomad AMI AF: 0.229

Gnomad AMR AF: 0.275

Gnomad ASJ AF: 0.214

Gnomad EAS AF: 0.672

Gnomad SAS AF: 0.345

Gnomad FIN AF: 0.216

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.221

Gnomad OTH AF: 0.200

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

GnomAD4 genome AF: 0.200 AC: 30433 AN: 152000 Hom.: 4253 Cov.: 32 AF XY: 0.207 AC XY: 15359 AN XY: 74270

African (AFR) AF: 0.0578 AC: 2397 AN: 41504

American (AMR) AF: 0.275 AC: 4200 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.214 AC: 742 AN: 3468

East Asian (EAS) AF: 0.673 AC: 3464 AN: 5150

South Asian (SAS) AF: 0.346 AC: 1664 AN: 4812

European-Finnish (FIN) AF: 0.216 AC: 2285 AN: 10572

Middle Eastern (MID) AF: 0.133 AC: 39 AN: 294

European-Non Finnish (NFE) AF: 0.221 AC: 15006 AN: 67938

Other (OTH) AF: 0.203 AC: 428 AN: 2104

Alfa AF: 0.210 Hom.: 492

Bravo AF: 0.200

Asia WGS AF: 0.457 AC: 1579 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.8
DANN	Benign	0.79
PhyloP100		0.23

Splicing

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

Other links and lift over

dbSNP: rs10508997; hg19: chr10-55482641;