chr10-4577595-T-G

Variant names:

• chr10-4577595-T-G
• rs10795189

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 0.179 in 152,140 control chromosomes in the GnomAD database, including 3,273 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 0.18 (3273 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.194
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.533 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.179 AC: 27226 AN: 152022 Hom.: 3270 Cov.: 33

Gnomad AFR AF: 0.276

Gnomad AMI AF: 0.0252

Gnomad AMR AF: 0.127

Gnomad ASJ AF: 0.110

Gnomad EAS AF: 0.550

Gnomad SAS AF: 0.234

Gnomad FIN AF: 0.0842

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.121

Gnomad OTH AF: 0.151

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

GnomAD4 genome AF: 0.179 AC: 27241 AN: 152140 Hom.: 3273 Cov.: 33 AF XY: 0.178 AC XY: 13246 AN XY: 74388

African (AFR) AF: 0.276 AC: 11462 AN: 41484

American (AMR) AF: 0.127 AC: 1949 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.110 AC: 382 AN: 3470

East Asian (EAS) AF: 0.550 AC: 2840 AN: 5162

South Asian (SAS) AF: 0.232 AC: 1119 AN: 4820

European-Finnish (FIN) AF: 0.0842 AC: 891 AN: 10586

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.121 AC: 8221 AN: 68006

Other (OTH) AF: 0.151 AC: 319 AN: 2110

Alfa AF: 0.136 Hom.: 813

Bravo AF: 0.185

Asia WGS AF: 0.360 AC: 1253 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	9.4
DANN	Benign	0.87
PhyloP100		0.19

Splicing

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

Other links and lift over

dbSNP: rs10795189; hg19: chr10-4619787;