6-29819295-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 0.88 in 152,212 control chromosomes in the GnomAD database, including 59,328 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 0.88 (59328 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.63

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.964 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: 0.880 AC: 133885 AN: 152094 Hom.: 59258 Cov.: 32

Gnomad AFR AF: 0.930

Gnomad AMI AF: 0.852

Gnomad AMR AF: 0.916

Gnomad ASJ AF: 0.905

Gnomad EAS AF: 0.986

Gnomad SAS AF: 0.938

Gnomad FIN AF: 0.726

Gnomad MID AF: 0.911

Gnomad NFE AF: 0.852

Gnomad OTH AF: 0.891

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

GnomAD4 genome AF: 0.880 AC: 134014 AN: 152212 Hom.: 59328 Cov.: 32 AF XY: 0.877 AC XY: 65222 AN XY: 74384

Gnomad4 AFR AF: 0.930

Gnomad4 AMR AF: 0.917

Gnomad4 ASJ AF: 0.905

Gnomad4 EAS AF: 0.986

Gnomad4 SAS AF: 0.938

Gnomad4 FIN AF: 0.726

Gnomad4 NFE AF: 0.852

Gnomad4 OTH AF: 0.893

Alfa AF: 0.866 Hom.: 32993

Bravo AF: 0.898

Asia WGS AF: 0.961 AC: 3343 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	0.52
Dann	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2743931; hg19: chr6-29787072;