rs6935921

Variant names:

• chr6-160687504-C-T
• rs6935921

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 0.64 in 151,892 control chromosomes in the GnomAD database, including 31,700 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 0.64 (31700 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.716
• Publications: 17 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.697 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: 0.640 AC: 97111 AN: 151776 Hom.: 31684 Cov.: 31

Gnomad AFR AF: 0.591

Gnomad AMI AF: 0.708

Gnomad AMR AF: 0.551

Gnomad ASJ AF: 0.707

Gnomad EAS AF: 0.361

Gnomad SAS AF: 0.509

Gnomad FIN AF: 0.726

Gnomad MID AF: 0.601

Gnomad NFE AF: 0.703

Gnomad OTH AF: 0.639

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

GnomAD4 genome AF: 0.640 AC: 97172 AN: 151892 Hom.: 31700 Cov.: 31 AF XY: 0.632 AC XY: 46933 AN XY: 74204

African (AFR) AF: 0.591 AC: 24453 AN: 41410

American (AMR) AF: 0.551 AC: 8412 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.707 AC: 2454 AN: 3470

East Asian (EAS) AF: 0.360 AC: 1859 AN: 5158

South Asian (SAS) AF: 0.509 AC: 2448 AN: 4808

European-Finnish (FIN) AF: 0.726 AC: 7652 AN: 10538

Middle Eastern (MID) AF: 0.595 AC: 175 AN: 294

European-Non Finnish (NFE) AF: 0.703 AC: 47719 AN: 67918

Other (OTH) AF: 0.641 AC: 1356 AN: 2114

Alfa AF: 0.673 Hom.: 115366

Bravo AF: 0.626

Asia WGS AF: 0.478 AC: 1667 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.62
DANN	Benign	0.14
PhyloP100		-0.72

Splicing

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

Other links and lift over

dbSNP: rs6935921; hg19: chr6-161108536;