6-29970119-C-T

Variant names:

• chr6-29970119-C-T
• rs3202637

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;