rs6914539

Variant names:

• chr6-103235862-C-T
• rs6914539

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 0.0379 in 151,956 control chromosomes in the GnomAD database, including 334 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 0.038 (334 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.118 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: 0.0378 AC: 5747 AN: 151840 Hom.: 332 Cov.: 32

Gnomad AFR AF: 0.121

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0179

Gnomad ASJ AF: 0.00374

Gnomad EAS AF: 0.00193

Gnomad SAS AF: 0.0330

Gnomad FIN AF: 0.000758

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.00346

Gnomad OTH AF: 0.0316

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

GnomAD4 genome AF: 0.0379 AC: 5766 AN: 151956 Hom.: 334 Cov.: 32 AF XY: 0.0373 AC XY: 2774 AN XY: 74286

African (AFR) AF: 0.121 AC: 4993 AN: 41424

American (AMR) AF: 0.0180 AC: 274 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.00374 AC: 13 AN: 3472

East Asian (EAS) AF: 0.00194 AC: 10 AN: 5156

South Asian (SAS) AF: 0.0336 AC: 162 AN: 4816

European-Finnish (FIN) AF: 0.000758 AC: 8 AN: 10554

Middle Eastern (MID) AF: 0.0136 AC: 4 AN: 294

European-Non Finnish (NFE) AF: 0.00346 AC: 235 AN: 67982

Other (OTH) AF: 0.0318 AC: 67 AN: 2108

Alfa AF: 0.0306 Hom.: 19

Bravo AF: 0.0437

Asia WGS AF: 0.0270 AC: 92 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.3
DANN	Benign	0.65
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs6914539; hg19: chr6-103683737;