6-29970119-C-T

Position:

• chr6-29970119-C-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 0.765 in 151,928 control chromosomes in the GnomAD database, including 44,664 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 0.77 (44664 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.921

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 (AMR) allele frequency at 95% confidence interval = 0.781 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: 0.765 AC: 116135 AN: 151814 Hom.: 44621 Cov.: 31

Gnomad AFR AF: 0.784

Gnomad AMI AF: 0.831

Gnomad AMR AF: 0.793

Gnomad ASJ AF: 0.640

Gnomad EAS AF: 0.698

Gnomad SAS AF: 0.714

Gnomad FIN AF: 0.817

Gnomad MID AF: 0.744

Gnomad NFE AF: 0.754

Gnomad OTH AF: 0.754

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

GnomAD4 genome AF: 0.765 AC: 116230 AN: 151928 Hom.: 44664 Cov.: 31 AF XY: 0.764 AC XY: 56772 AN XY: 74288

Gnomad4 AFR AF: 0.784

Gnomad4 AMR AF: 0.793

Gnomad4 ASJ AF: 0.640

Gnomad4 EAS AF: 0.699

Gnomad4 SAS AF: 0.712

Gnomad4 FIN AF: 0.817

Gnomad4 NFE AF: 0.754

Gnomad4 OTH AF: 0.757

Alfa AF: 0.753 Hom.: 47986

Bravo AF: 0.769

Asia WGS AF: 0.743 AC: 2585 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	2.2
DANN	Benign	0.19

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3202637; hg19: chr6-29937896;