chr6-94315304-G-C

Position:

• chr6-94315304-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 0.133 in 151,958 control chromosomes in the GnomAD database, including 2,131 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 0.13 (2131 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.769

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.293 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.132 AC: 20084 AN: 151838 Hom.: 2113 Cov.: 31

Gnomad AFR AF: 0.297

Gnomad AMI AF: 0.116

Gnomad AMR AF: 0.0843

Gnomad ASJ AF: 0.0841

Gnomad EAS AF: 0.0525

Gnomad SAS AF: 0.0911

Gnomad FIN AF: 0.0388

Gnomad MID AF: 0.135

Gnomad NFE AF: 0.0693

Gnomad OTH AF: 0.120

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

GnomAD4 genome AF: 0.133 AC: 20137 AN: 151958 Hom.: 2131 Cov.: 31 AF XY: 0.130 AC XY: 9627 AN XY: 74268

Gnomad4 AFR AF: 0.298

Gnomad4 AMR AF: 0.0843

Gnomad4 ASJ AF: 0.0841

Gnomad4 EAS AF: 0.0526

Gnomad4 SAS AF: 0.0909

Gnomad4 FIN AF: 0.0388

Gnomad4 NFE AF: 0.0693

Gnomad4 OTH AF: 0.119

Alfa AF: 0.0189 Hom.: 10

Bravo AF: 0.143

Asia WGS AF: 0.0980 AC: 345 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.15
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs441859; hg19: chr6-95025022; COSMIC: COSV69413961;