rs6934903

Variant names:

• chr6-135130426-T-A
• rs6934903

Your query was ambiguous. Multiple possible variants found:

• chr6-135130426-T-A
• chr6-135130426-T-C

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 0.146 in 152,154 control chromosomes in the GnomAD database, including 2,031 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 0.15 (2031 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.258
• Publications: 13 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.245 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: 0.146 AC: 22230 AN: 152036 Hom.: 2033 Cov.: 31

Gnomad AFR AF: 0.0435

Gnomad AMI AF: 0.0735

Gnomad AMR AF: 0.145

Gnomad ASJ AF: 0.183

Gnomad EAS AF: 0.257

Gnomad SAS AF: 0.132

Gnomad FIN AF: 0.247

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.186

Gnomad OTH AF: 0.132

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

GnomAD4 genome AF: 0.146 AC: 22228 AN: 152154 Hom.: 2031 Cov.: 31 AF XY: 0.148 AC XY: 10992 AN XY: 74370

African (AFR) AF: 0.0436 AC: 1810 AN: 41546

American (AMR) AF: 0.145 AC: 2208 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.183 AC: 635 AN: 3472

East Asian (EAS) AF: 0.257 AC: 1325 AN: 5158

South Asian (SAS) AF: 0.132 AC: 637 AN: 4818

European-Finnish (FIN) AF: 0.247 AC: 2609 AN: 10574

Middle Eastern (MID) AF: 0.153 AC: 45 AN: 294

European-Non Finnish (NFE) AF: 0.186 AC: 12618 AN: 67990

Other (OTH) AF: 0.130 AC: 274 AN: 2112

Alfa AF: 0.169 Hom.: 320

Bravo AF: 0.136

Asia WGS AF: 0.171 AC: 593 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.6
DANN	Benign	0.50
PhyloP100		-0.26

Splicing

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

Other links and lift over

dbSNP: rs6934903; hg19: chr6-135451564; COSMIC: COSV58836606;