chr10-95092933-T-A

Variant names:

• chr10-95092933-T-A
• rs72820627

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

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 0.26 (0 hom., cov: 37)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.48
• Publications: 2 publications found

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).

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: 0.257 AC: 30824 AN: 119842 Hom.: 0 Cov.: 37

Gnomad AFR AF: 0.138

Gnomad AMI AF: 0.278

Gnomad AMR AF: 0.225

Gnomad ASJ AF: 0.335

Gnomad EAS AF: 0.249

Gnomad SAS AF: 0.253

Gnomad FIN AF: 0.321

Gnomad MID AF: 0.319

Gnomad NFE AF: 0.334

Gnomad OTH AF: 0.266

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

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR;InbreedingCoeff AF: 0.257 AC: 30832 AN: 119950 Hom.: 0 Cov.: 37 AF XY: 0.181 AC XY: 10515 AN XY: 57980

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.138 AC: 4903 AN: 35564

American (AMR) AF: 0.225 AC: 2697 AN: 11980

Ashkenazi Jewish (ASJ) AF: 0.335 AC: 878 AN: 2624

East Asian (EAS) AF: 0.249 AC: 1044 AN: 4196

South Asian (SAS) AF: 0.252 AC: 934 AN: 3704

European-Finnish (FIN) AF: 0.321 AC: 2525 AN: 7878

Middle Eastern (MID) AF: 0.304 AC: 65 AN: 214

European-Non Finnish (NFE) AF: 0.334 AC: 17160 AN: 51452

Other (OTH) AF: 0.264 AC: 437 AN: 1658

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0.000000), which strongly suggests a high chance of mosaicism in these individuals.

Alfa AF: 0.331 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	1.7
DANN	Benign	0.63
PhyloP100		-3.5

Splicing

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

Other links and lift over

dbSNP: rs72820627; hg19: chr10-96852690; COSMIC: COSV59693649;