chr6-115778745-C-T

Variant names:

• chr6-115778745-C-T
• rs9374571

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 0.498 in 152,066 control chromosomes in the GnomAD database, including 21,712 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 0.50 (21712 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0940

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.616 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: 0.498 AC: 75699 AN: 151948 Hom.: 21704 Cov.: 33

Gnomad AFR AF: 0.197

Gnomad AMI AF: 0.495

Gnomad AMR AF: 0.594

Gnomad ASJ AF: 0.543

Gnomad EAS AF: 0.580

Gnomad SAS AF: 0.470

Gnomad FIN AF: 0.704

Gnomad MID AF: 0.560

Gnomad NFE AF: 0.620

Gnomad OTH AF: 0.518

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

GnomAD4 genome AF: 0.498 AC: 75724 AN: 152066 Hom.: 21712 Cov.: 33 AF XY: 0.502 AC XY: 37330 AN XY: 74328

Gnomad4 AFR AF: 0.197

Gnomad4 AMR AF: 0.594

Gnomad4 ASJ AF: 0.543

Gnomad4 EAS AF: 0.579

Gnomad4 SAS AF: 0.470

Gnomad4 FIN AF: 0.704

Gnomad4 NFE AF: 0.621

Gnomad4 OTH AF: 0.519

Alfa AF: 0.577 Hom.: 14692

Bravo AF: 0.478

Asia WGS AF: 0.502 AC: 1748 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.4
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9374571; hg19: chr6-116099909;