chr6-165199369-T-C

Variant names:

• chr6-165199369-T-C
• rs1764053

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 0.425 in 152,026 control chromosomes in the GnomAD database, including 15,192 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 0.42 (15192 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0420
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.624 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: 0.424 AC: 64469 AN: 151908 Hom.: 15152 Cov.: 32

Gnomad AFR AF: 0.630

Gnomad AMI AF: 0.201

Gnomad AMR AF: 0.463

Gnomad ASJ AF: 0.303

Gnomad EAS AF: 0.367

Gnomad SAS AF: 0.261

Gnomad FIN AF: 0.374

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.324

Gnomad OTH AF: 0.419

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

GnomAD4 genome AF: 0.425 AC: 64570 AN: 152026 Hom.: 15192 Cov.: 32 AF XY: 0.425 AC XY: 31555 AN XY: 74304

African (AFR) AF: 0.630 AC: 26133 AN: 41470

American (AMR) AF: 0.463 AC: 7063 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.303 AC: 1051 AN: 3470

East Asian (EAS) AF: 0.368 AC: 1895 AN: 5156

South Asian (SAS) AF: 0.262 AC: 1260 AN: 4818

European-Finnish (FIN) AF: 0.374 AC: 3949 AN: 10552

Middle Eastern (MID) AF: 0.497 AC: 145 AN: 292

European-Non Finnish (NFE) AF: 0.324 AC: 22007 AN: 67978

Other (OTH) AF: 0.419 AC: 884 AN: 2108

Alfa AF: 0.364 Hom.: 27114

Bravo AF: 0.442

Asia WGS AF: 0.348 AC: 1210 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.5
DANN	Benign	0.61
PhyloP100		0.042

Splicing

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

Other links and lift over

dbSNP: rs1764053; hg19: chr6-165612858; COSMIC: COSV69433316;