rs6903874

Variant names:

• chr6-132575771-T-C
• rs6903874

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 0.231 in 152,086 control chromosomes in the GnomAD database, including 4,398 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 0.23 (4398 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0560
• Publications: 13 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.309 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.231 AC: 35129 AN: 151968 Hom.: 4386 Cov.: 32

Gnomad AFR AF: 0.313

Gnomad AMI AF: 0.259

Gnomad AMR AF: 0.234

Gnomad ASJ AF: 0.175

Gnomad EAS AF: 0.149

Gnomad SAS AF: 0.147

Gnomad FIN AF: 0.232

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.196

Gnomad OTH AF: 0.217

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

GnomAD4 genome AF: 0.231 AC: 35183 AN: 152086 Hom.: 4398 Cov.: 32 AF XY: 0.230 AC XY: 17111 AN XY: 74344

African (AFR) AF: 0.313 AC: 12997 AN: 41482

American (AMR) AF: 0.234 AC: 3577 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.175 AC: 606 AN: 3466

East Asian (EAS) AF: 0.150 AC: 776 AN: 5182

South Asian (SAS) AF: 0.147 AC: 711 AN: 4826

European-Finnish (FIN) AF: 0.232 AC: 2452 AN: 10558

Middle Eastern (MID) AF: 0.194 AC: 57 AN: 294

European-Non Finnish (NFE) AF: 0.196 AC: 13307 AN: 67972

Other (OTH) AF: 0.219 AC: 464 AN: 2116

Alfa AF: 0.233 Hom.: 573

Bravo AF: 0.236

Asia WGS AF: 0.189 AC: 658 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	8.0
DANN	Benign	0.90
PhyloP100		0.056

Splicing

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

Other links and lift over

dbSNP: rs6903874; hg19: chr6-132896910; COSMIC: COSV51584239;