rs6935921

Variant names:

• chr6-160687504-C-T
• rs6935921

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.591

Gnomad4 AMR AF: 0.551

Gnomad4 ASJ AF: 0.707

Gnomad4 EAS AF: 0.360

Gnomad4 SAS AF: 0.509

Gnomad4 FIN AF: 0.726

Gnomad4 NFE AF: 0.703

Gnomad4 OTH AF: 0.641

Alfa AF: 0.686 Hom.: 73699

Bravo AF: 0.626

Asia WGS AF: 0.478 AC: 1667 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6935921; hg19: chr6-161108536;