6-29767916-A-G

Position:

• chr6-29767916-A-G

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 0.658 in 151,520 control chromosomes in the GnomAD database, including 30,124 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 0.66 (30124 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -5.76

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.07).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.699 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.658 AC: 99602 AN: 151404 Hom.: 30103 Cov.: 33

Gnomad AFR AF: 0.706

Gnomad AMI AF: 0.590

Gnomad AMR AF: 0.633

Gnomad ASJ AF: 0.679

Gnomad EAS AF: 0.499

Gnomad SAS AF: 0.522

Gnomad FIN AF: 0.566

Gnomad MID AF: 0.656

Gnomad NFE AF: 0.670

Gnomad OTH AF: 0.652

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

GnomAD4 genome AF: 0.658 AC: 99666 AN: 151520 Hom.: 30124 Cov.: 33 AF XY: 0.650 AC XY: 48110 AN XY: 74026

Gnomad4 AFR AF: 0.706

Gnomad4 AMR AF: 0.633

Gnomad4 ASJ AF: 0.679

Gnomad4 EAS AF: 0.500

Gnomad4 SAS AF: 0.522

Gnomad4 FIN AF: 0.566

Gnomad4 NFE AF: 0.670

Gnomad4 OTH AF: 0.644

Alfa AF: 0.700 Hom.: 17025

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.017
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: rs1737046; hg19: chr6-29735693;