rs10245440

Variant names:

• chr7-21422914-C-A
• rs10245440

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 0.273 in 152,088 control chromosomes in the GnomAD database, including 6,164 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 0.27 (6164 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00400
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.522 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: 0.273 AC: 41517 AN: 151970 Hom.: 6147 Cov.: 31

Gnomad AFR AF: 0.349

Gnomad AMI AF: 0.0724

Gnomad AMR AF: 0.231

Gnomad ASJ AF: 0.151

Gnomad EAS AF: 0.539

Gnomad SAS AF: 0.290

Gnomad FIN AF: 0.254

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.228

Gnomad OTH AF: 0.248

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

GnomAD4 genome AF: 0.273 AC: 41581 AN: 152088 Hom.: 6164 Cov.: 31 AF XY: 0.275 AC XY: 20411 AN XY: 74338

African (AFR) AF: 0.350 AC: 14494 AN: 41454

American (AMR) AF: 0.230 AC: 3527 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.151 AC: 522 AN: 3468

East Asian (EAS) AF: 0.539 AC: 2782 AN: 5166

South Asian (SAS) AF: 0.290 AC: 1400 AN: 4822

European-Finnish (FIN) AF: 0.254 AC: 2686 AN: 10572

Middle Eastern (MID) AF: 0.170 AC: 50 AN: 294

European-Non Finnish (NFE) AF: 0.228 AC: 15520 AN: 67984

Other (OTH) AF: 0.253 AC: 534 AN: 2114

Alfa AF: 0.252 Hom.: 1873

Bravo AF: 0.277

Asia WGS AF: 0.441 AC: 1532 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	2.8
DANN	Benign	0.51
PhyloP100		-0.0040

Splicing

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

Other links and lift over

dbSNP: rs10245440; hg19: chr7-21462532;