chr6-95885976-A-C

Position:

• chr6-95885976-A-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 0.657 in 151,970 control chromosomes in the GnomAD database, including 33,105 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 0.66 (33105 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.17

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.686 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: 0.657 AC: 99791 AN: 151852 Hom.: 33071 Cov.: 31

Gnomad AFR AF: 0.662

Gnomad AMI AF: 0.633

Gnomad AMR AF: 0.544

Gnomad ASJ AF: 0.660

Gnomad EAS AF: 0.477

Gnomad SAS AF: 0.693

Gnomad FIN AF: 0.656

Gnomad MID AF: 0.696

Gnomad NFE AF: 0.691

Gnomad OTH AF: 0.657

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

GnomAD4 genome AF: 0.657 AC: 99871 AN: 151970 Hom.: 33105 Cov.: 31 AF XY: 0.650 AC XY: 48266 AN XY: 74262

Gnomad4 AFR AF: 0.662

Gnomad4 AMR AF: 0.544

Gnomad4 ASJ AF: 0.660

Gnomad4 EAS AF: 0.477

Gnomad4 SAS AF: 0.694

Gnomad4 FIN AF: 0.656

Gnomad4 NFE AF: 0.691

Gnomad4 OTH AF: 0.655

Alfa AF: 0.657 Hom.: 5218

Bravo AF: 0.647

Asia WGS AF: 0.613 AC: 2134 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2799652; hg19: chr6-96333852;