chr6-75746331-G-C

Position:

• chr6-75746331-G-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 0.0877 in 152,152 control chromosomes in the GnomAD database, including 777 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 0.088 (777 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.238

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.281 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: 0.0877 AC: 13329 AN: 152034 Hom.: 777 Cov.: 32

Gnomad AFR AF: 0.114

Gnomad AMI AF: 0.0121

Gnomad AMR AF: 0.0769

Gnomad ASJ AF: 0.0378

Gnomad EAS AF: 0.294

Gnomad SAS AF: 0.111

Gnomad FIN AF: 0.0839

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0607

Gnomad OTH AF: 0.0948

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

GnomAD4 genome AF: 0.0877 AC: 13339 AN: 152152 Hom.: 777 Cov.: 32 AF XY: 0.0888 AC XY: 6603 AN XY: 74388

Gnomad4 AFR AF: 0.114

Gnomad4 AMR AF: 0.0767

Gnomad4 ASJ AF: 0.0378

Gnomad4 EAS AF: 0.294

Gnomad4 SAS AF: 0.111

Gnomad4 FIN AF: 0.0839

Gnomad4 NFE AF: 0.0607

Gnomad4 OTH AF: 0.0953

Alfa AF: 0.0710 Hom.: 57

Bravo AF: 0.0903

Asia WGS AF: 0.190 AC: 658 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.6
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs276699; hg19: chr6-76456048;