rs6930229

Positions:

• chr6-159862407-A-C
• chr6-159862407-A-T

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 0.637 in 151,962 control chromosomes in the GnomAD database, including 31,180 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 (31180 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.08

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.672 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.637 AC: 96767 AN: 151846 Hom.: 31175 Cov.: 31

Gnomad AFR AF: 0.633

Gnomad AMI AF: 0.555

Gnomad AMR AF: 0.597

Gnomad ASJ AF: 0.670

Gnomad EAS AF: 0.346

Gnomad SAS AF: 0.656

Gnomad FIN AF: 0.580

Gnomad MID AF: 0.734

Gnomad NFE AF: 0.677

Gnomad OTH AF: 0.661

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

GnomAD4 genome AF: 0.637 AC: 96798 AN: 151962 Hom.: 31180 Cov.: 31 AF XY: 0.629 AC XY: 46734 AN XY: 74272

Gnomad4 AFR AF: 0.633

Gnomad4 AMR AF: 0.596

Gnomad4 ASJ AF: 0.670

Gnomad4 EAS AF: 0.346

Gnomad4 SAS AF: 0.656

Gnomad4 FIN AF: 0.580

Gnomad4 NFE AF: 0.677

Gnomad4 OTH AF: 0.655

Alfa AF: 0.658 Hom.: 16575

Bravo AF: 0.636

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.64
DANN	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6930229; hg19: chr6-160283439;