6-29721813-T-G

Position:

• chr6-29721813-T-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 0.179 in 152,210 control chromosomes in the GnomAD database, including 2,862 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 0.18 (2862 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.46

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.06).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.285 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: 0.179 AC: 27192 AN: 152092 Hom.: 2853 Cov.: 32

Gnomad AFR AF: 0.257

Gnomad AMI AF: 0.169

Gnomad AMR AF: 0.190

Gnomad ASJ AF: 0.179

Gnomad EAS AF: 0.297

Gnomad SAS AF: 0.297

Gnomad FIN AF: 0.107

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.123

Gnomad OTH AF: 0.180

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

GnomAD4 genome AF: 0.179 AC: 27228 AN: 152210 Hom.: 2862 Cov.: 32 AF XY: 0.181 AC XY: 13485 AN XY: 74426

Gnomad4 AFR AF: 0.257

Gnomad4 AMR AF: 0.190

Gnomad4 ASJ AF: 0.179

Gnomad4 EAS AF: 0.298

Gnomad4 SAS AF: 0.298

Gnomad4 FIN AF: 0.107

Gnomad4 NFE AF: 0.123

Gnomad4 OTH AF: 0.178

Alfa AF: 0.132 Hom.: 1638

Bravo AF: 0.186

Asia WGS AF: 0.223 AC: 773 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.43
DANN	Benign	0.23

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9258170; hg19: chr6-29689590; COSMIC: COSV52577386;