6-65855460-G-A

Position:

• chr6-65855460-G-A

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 151,932 control chromosomes in the GnomAD database, including 32,833 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 0.65 (32833 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0550

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.847 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: 0.654 AC: 99346 AN: 151812 Hom.: 32793 Cov.: 32

Gnomad AFR AF: 0.625

Gnomad AMI AF: 0.597

Gnomad AMR AF: 0.718

Gnomad ASJ AF: 0.696

Gnomad EAS AF: 0.868

Gnomad SAS AF: 0.792

Gnomad FIN AF: 0.646

Gnomad MID AF: 0.677

Gnomad NFE AF: 0.632

Gnomad OTH AF: 0.661

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

GnomAD4 genome AF: 0.655 AC: 99442 AN: 151932 Hom.: 32833 Cov.: 32 AF XY: 0.663 AC XY: 49232 AN XY: 74234

Gnomad4 AFR AF: 0.625

Gnomad4 AMR AF: 0.718

Gnomad4 ASJ AF: 0.696

Gnomad4 EAS AF: 0.868

Gnomad4 SAS AF: 0.791

Gnomad4 FIN AF: 0.646

Gnomad4 NFE AF: 0.632

Gnomad4 OTH AF: 0.664

Alfa AF: 0.647 Hom.: 36789

Bravo AF: 0.659

Asia WGS AF: 0.812 AC: 2821 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.89
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9354308; hg19: chr6-66565353;