6-32604474-T-C

Variant names:

• chr6-32604474-T-C
• rs2858870

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 0.119 in 152,156 control chromosomes in the GnomAD database, including 1,206 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 0.12 (1206 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.838
• Publications: 55 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.158 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: 0.120 AC: 18175 AN: 152038 Hom.: 1210 Cov.: 31

Gnomad AFR AF: 0.127

Gnomad AMI AF: 0.224

Gnomad AMR AF: 0.103

Gnomad ASJ AF: 0.123

Gnomad EAS AF: 0.0424

Gnomad SAS AF: 0.169

Gnomad FIN AF: 0.0506

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.130

Gnomad OTH AF: 0.135

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

GnomAD4 genome AF: 0.119 AC: 18172 AN: 152156 Hom.: 1206 Cov.: 31 AF XY: 0.116 AC XY: 8597 AN XY: 74394

African (AFR) AF: 0.127 AC: 5263 AN: 41472

American (AMR) AF: 0.103 AC: 1575 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.123 AC: 428 AN: 3468

East Asian (EAS) AF: 0.0426 AC: 221 AN: 5182

South Asian (SAS) AF: 0.168 AC: 809 AN: 4818

European-Finnish (FIN) AF: 0.0506 AC: 536 AN: 10602

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.130 AC: 8822 AN: 67996

Other (OTH) AF: 0.133 AC: 281 AN: 2114

Alfa AF: 0.121 Hom.: 1363

Bravo AF: 0.126

Asia WGS AF: 0.0780 AC: 270 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	9.6
DANN	Benign	0.67
PhyloP100		0.84

Splicing

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

Other links and lift over

dbSNP: rs2858870; hg19: chr6-32572251;