rs846951

chr6-107697078-G-A

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 0.681 in 152,040 control chromosomes in the GnomAD database, including 35,607 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 0.68 (35607 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.355

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 (AFR) allele frequency at 95% confidence interval = 0.77 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: 0.681 AC: 103478 AN: 151922 Hom.: 35573 Cov.: 31

Gnomad AFR AF: 0.777

Gnomad AMI AF: 0.647

Gnomad AMR AF: 0.631

Gnomad ASJ AF: 0.700

Gnomad EAS AF: 0.570

Gnomad SAS AF: 0.630

Gnomad FIN AF: 0.577

Gnomad MID AF: 0.693

Gnomad NFE AF: 0.662

Gnomad OTH AF: 0.662

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

GnomAD4 genome AF: 0.681 AC: 103568 AN: 152040 Hom.: 35607 Cov.: 31 AF XY: 0.676 AC XY: 50220 AN XY: 74296

Gnomad4 AFR AF: 0.777

Gnomad4 AMR AF: 0.631

Gnomad4 ASJ AF: 0.700

Gnomad4 EAS AF: 0.570

Gnomad4 SAS AF: 0.631

Gnomad4 FIN AF: 0.577

Gnomad4 NFE AF: 0.662

Gnomad4 OTH AF: 0.664

Alfa AF: 0.685 Hom.: 6821

Bravo AF: 0.685

Asia WGS AF: 0.618 AC: 2152 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	3.5
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: rs846951; hg19: chr6-108018282;