chr5-132100793-G-T

Variant names:

• chr5-132100793-G-T
• rs10065787

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 0.335 in 152,104 control chromosomes in the GnomAD database, including 9,672 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 0.33 (9672 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.867
• Publications: 14 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.438 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: 0.335 AC: 50944 AN: 151986 Hom.: 9674 Cov.: 32

Gnomad AFR AF: 0.179

Gnomad AMI AF: 0.595

Gnomad AMR AF: 0.318

Gnomad ASJ AF: 0.333

Gnomad EAS AF: 0.208

Gnomad SAS AF: 0.156

Gnomad FIN AF: 0.399

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.443

Gnomad OTH AF: 0.369

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

GnomAD4 genome AF: 0.335 AC: 50943 AN: 152104 Hom.: 9672 Cov.: 32 AF XY: 0.326 AC XY: 24246 AN XY: 74366

African (AFR) AF: 0.179 AC: 7431 AN: 41520

American (AMR) AF: 0.318 AC: 4855 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.333 AC: 1152 AN: 3464

East Asian (EAS) AF: 0.208 AC: 1078 AN: 5178

South Asian (SAS) AF: 0.155 AC: 748 AN: 4826

European-Finnish (FIN) AF: 0.399 AC: 4212 AN: 10564

Middle Eastern (MID) AF: 0.269 AC: 79 AN: 294

European-Non Finnish (NFE) AF: 0.443 AC: 30081 AN: 67954

Other (OTH) AF: 0.364 AC: 767 AN: 2108

Alfa AF: 0.409 Hom.: 50333

Bravo AF: 0.328

Asia WGS AF: 0.183 AC: 636 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	7.3
DANN	Benign	0.52
PhyloP100		0.87

Splicing

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

Other links and lift over

dbSNP: rs10065787; hg19: chr5-131436486; COSMIC: COSV60199034;