6-29950322-G-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 0.655 in 150,796 control chromosomes in the GnomAD database, including 32,455 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 (32455 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0900

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.741 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: 0.655 AC: 98694 AN: 150678 Hom.: 32398 Cov.: 31

Gnomad AFR AF: 0.705

Gnomad AMI AF: 0.582

Gnomad AMR AF: 0.752

Gnomad ASJ AF: 0.696

Gnomad EAS AF: 0.686

Gnomad SAS AF: 0.627

Gnomad FIN AF: 0.606

Gnomad MID AF: 0.673

Gnomad NFE AF: 0.609

Gnomad OTH AF: 0.671

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

GnomAD4 genome AF: 0.655 AC: 98802 AN: 150796 Hom.: 32455 Cov.: 31 AF XY: 0.655 AC XY: 48261 AN XY: 73696

Gnomad4 AFR AF: 0.705

Gnomad4 AMR AF: 0.752

Gnomad4 ASJ AF: 0.696

Gnomad4 EAS AF: 0.686

Gnomad4 SAS AF: 0.628

Gnomad4 FIN AF: 0.606

Gnomad4 NFE AF: 0.609

Gnomad4 OTH AF: 0.674

Alfa AF: 0.591 Hom.: 11533

Asia WGS AF: 0.710 AC: 2463 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	3.2
Dann	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2517713; hg19: chr6-29918099;