6-39733974-A-G

Position:

• chr6-39733974-A-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 0.568 in 152,062 control chromosomes in the GnomAD database, including 25,864 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 0.57 (25864 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.866

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.751 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: 0.568 AC: 86262 AN: 151942 Hom.: 25831 Cov.: 32

Gnomad AFR AF: 0.758

Gnomad AMI AF: 0.458

Gnomad AMR AF: 0.557

Gnomad ASJ AF: 0.396

Gnomad EAS AF: 0.639

Gnomad SAS AF: 0.605

Gnomad FIN AF: 0.451

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.475

Gnomad OTH AF: 0.561

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

GnomAD4 genome AF: 0.568 AC: 86342 AN: 152062 Hom.: 25864 Cov.: 32 AF XY: 0.568 AC XY: 42237 AN XY: 74332

Gnomad4 AFR AF: 0.758

Gnomad4 AMR AF: 0.557

Gnomad4 ASJ AF: 0.396

Gnomad4 EAS AF: 0.640

Gnomad4 SAS AF: 0.606

Gnomad4 FIN AF: 0.451

Gnomad4 NFE AF: 0.475

Gnomad4 OTH AF: 0.556

Alfa AF: 0.532 Hom.: 3997

Bravo AF: 0.582

Asia WGS AF: 0.607 AC: 2111 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.22
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs215497; hg19: chr6-39701750;