6-41396517-C-T

Variant names:

• chr6-41396517-C-T
• rs1535582

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 0.599 in 151,856 control chromosomes in the GnomAD database, including 27,304 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 0.60 (27304 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.641

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 = 0.646 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: 0.598 AC: 90794 AN: 151738 Hom.: 27262 Cov.: 30

Gnomad AFR AF: 0.601

Gnomad AMI AF: 0.432

Gnomad AMR AF: 0.656

Gnomad ASJ AF: 0.539

Gnomad EAS AF: 0.605

Gnomad SAS AF: 0.569

Gnomad FIN AF: 0.596

Gnomad MID AF: 0.567

Gnomad NFE AF: 0.592

Gnomad OTH AF: 0.560

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

GnomAD4 genome AF: 0.599 AC: 90894 AN: 151856 Hom.: 27304 Cov.: 30 AF XY: 0.600 AC XY: 44519 AN XY: 74238

Gnomad4 AFR AF: 0.602

Gnomad4 AMR AF: 0.657

Gnomad4 ASJ AF: 0.539

Gnomad4 EAS AF: 0.605

Gnomad4 SAS AF: 0.569

Gnomad4 FIN AF: 0.596

Gnomad4 NFE AF: 0.592

Gnomad4 OTH AF: 0.561

Alfa AF: 0.581 Hom.: 37006

Bravo AF: 0.604

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.35
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1535582; hg19: chr6-41364255;