chr10-95580173-G-A

Variant names:

• chr10-95580173-G-A
• rs7895441

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 0.253 in 152,070 control chromosomes in the GnomAD database, including 5,645 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 0.25 (5645 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.58
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.388 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.253 AC: 38485 AN: 151952 Hom.: 5645 Cov.: 32

Gnomad AFR AF: 0.394

Gnomad AMI AF: 0.237

Gnomad AMR AF: 0.189

Gnomad ASJ AF: 0.380

Gnomad EAS AF: 0.206

Gnomad SAS AF: 0.226

Gnomad FIN AF: 0.137

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.198

Gnomad OTH AF: 0.279

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

GnomAD4 genome AF: 0.253 AC: 38511 AN: 152070 Hom.: 5645 Cov.: 32 AF XY: 0.250 AC XY: 18607 AN XY: 74324

African (AFR) AF: 0.393 AC: 16297 AN: 41456

American (AMR) AF: 0.189 AC: 2891 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.380 AC: 1314 AN: 3462

East Asian (EAS) AF: 0.206 AC: 1066 AN: 5168

South Asian (SAS) AF: 0.227 AC: 1093 AN: 4818

European-Finnish (FIN) AF: 0.137 AC: 1447 AN: 10588

Middle Eastern (MID) AF: 0.357 AC: 105 AN: 294

European-Non Finnish (NFE) AF: 0.199 AC: 13494 AN: 67980

Other (OTH) AF: 0.279 AC: 588 AN: 2110

Alfa AF: 0.221 Hom.: 11790

Bravo AF: 0.262

Asia WGS AF: 0.223 AC: 777 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.35
DANN	Benign	0.39
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs7895441; hg19: chr10-97339930;