rs10272724

Variant names:

• chr7-50409515-T-C
• rs10272724

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 0.239 in 151,760 control chromosomes in the GnomAD database, including 4,597 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 0.24 (4597 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.468
• Publications: 36 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.269 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: 0.239 AC: 36296 AN: 151642 Hom.: 4594 Cov.: 32

Gnomad AFR AF: 0.179

Gnomad AMI AF: 0.292

Gnomad AMR AF: 0.233

Gnomad ASJ AF: 0.219

Gnomad EAS AF: 0.106

Gnomad SAS AF: 0.281

Gnomad FIN AF: 0.326

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.271

Gnomad OTH AF: 0.247

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

GnomAD4 genome AF: 0.239 AC: 36316 AN: 151760 Hom.: 4597 Cov.: 32 AF XY: 0.243 AC XY: 18034 AN XY: 74170

African (AFR) AF: 0.179 AC: 7391 AN: 41354

American (AMR) AF: 0.233 AC: 3557 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.219 AC: 759 AN: 3472

East Asian (EAS) AF: 0.106 AC: 547 AN: 5150

South Asian (SAS) AF: 0.281 AC: 1354 AN: 4814

European-Finnish (FIN) AF: 0.326 AC: 3438 AN: 10540

Middle Eastern (MID) AF: 0.279 AC: 82 AN: 294

European-Non Finnish (NFE) AF: 0.271 AC: 18411 AN: 67868

Other (OTH) AF: 0.243 AC: 512 AN: 2104

Alfa AF: 0.259 Hom.: 2815

Bravo AF: 0.231

Asia WGS AF: 0.169 AC: 589 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.3
DANN	Benign	0.52
PhyloP100		-0.47

Splicing

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

Other links and lift over

dbSNP: rs10272724; hg19: chr7-50477213;