chr6-65905462-T-C

Variant names:

• chr6-65905462-T-C
• rs1587434

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;