6-11625694-A-G

Variant names:

• chr6-11625694-A-G
• rs715793

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 0.941 in 152,262 control chromosomes in the GnomAD database, including 67,472 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 0.94 (67472 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.101

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.59).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.941 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: 0.941 AC: 143194 AN: 152144 Hom.: 67422 Cov.: 31

Gnomad AFR AF: 0.927

Gnomad AMI AF: 0.968

Gnomad AMR AF: 0.937

Gnomad ASJ AF: 0.971

Gnomad EAS AF: 0.963

Gnomad SAS AF: 0.943

Gnomad FIN AF: 0.945

Gnomad MID AF: 0.981

Gnomad NFE AF: 0.946

Gnomad OTH AF: 0.951

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

GnomAD4 genome AF: 0.941 AC: 143303 AN: 152262 Hom.: 67472 Cov.: 31 AF XY: 0.941 AC XY: 70052 AN XY: 74440

Gnomad4 AFR AF: 0.928

Gnomad4 AMR AF: 0.937

Gnomad4 ASJ AF: 0.971

Gnomad4 EAS AF: 0.963

Gnomad4 SAS AF: 0.943

Gnomad4 FIN AF: 0.945

Gnomad4 NFE AF: 0.946

Gnomad4 OTH AF: 0.952

Alfa AF: 0.943 Hom.: 21671

Bravo AF: 0.940

Asia WGS AF: 0.960 AC: 3341 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.59
CADD	Benign	14
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: rs715793; hg19: chr6-11625927;