6-65905462-T-C

Position:

• chr6-65905462-T-C

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 0.91 in 151,112 control chromosomes in the GnomAD database, including 63,326 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 0.91 (63326 hom., cov: 27)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.79

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.974 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: 0.910 AC: 137382 AN: 150994 Hom.: 63279 Cov.: 27

Gnomad AFR AF: 0.739

Gnomad AMI AF: 0.962

Gnomad AMR AF: 0.935

Gnomad ASJ AF: 0.997

Gnomad EAS AF: 0.933

Gnomad SAS AF: 0.984

Gnomad FIN AF: 0.996

Gnomad MID AF: 0.978

Gnomad NFE AF: 0.980

Gnomad OTH AF: 0.941

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

GnomAD4 genome AF: 0.910 AC: 137485 AN: 151112 Hom.: 63326 Cov.: 27 AF XY: 0.913 AC XY: 67455 AN XY: 73852

Gnomad4 AFR AF: 0.739

Gnomad4 AMR AF: 0.935

Gnomad4 ASJ AF: 0.997

Gnomad4 EAS AF: 0.933

Gnomad4 SAS AF: 0.984

Gnomad4 FIN AF: 0.996

Gnomad4 NFE AF: 0.980

Gnomad4 OTH AF: 0.942

Alfa AF: 0.951 Hom.: 3385

Bravo AF: 0.895

Asia WGS AF: 0.949 AC: 3301 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.3
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1587434; hg19: chr6-66615355;