chr6-95615593-A-G

Variant names:

• chr6-95615593-A-G
• rs9387605

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.597 in 152,086 control chromosomes in the GnomAD database, including 27,512 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 0.60 (27512 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.27
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.846 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: 0.597 AC: 90739 AN: 151968 Hom.: 27498 Cov.: 33

Gnomad AFR AF: 0.623

Gnomad AMI AF: 0.530

Gnomad AMR AF: 0.533

Gnomad ASJ AF: 0.595

Gnomad EAS AF: 0.867

Gnomad SAS AF: 0.732

Gnomad FIN AF: 0.529

Gnomad MID AF: 0.696

Gnomad NFE AF: 0.576

Gnomad OTH AF: 0.617

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

GnomAD4 genome AF: 0.597 AC: 90791 AN: 152086 Hom.: 27512 Cov.: 33 AF XY: 0.596 AC XY: 44266 AN XY: 74334

African (AFR) AF: 0.622 AC: 25819 AN: 41498

American (AMR) AF: 0.532 AC: 8133 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.595 AC: 2061 AN: 3466

East Asian (EAS) AF: 0.867 AC: 4482 AN: 5168

South Asian (SAS) AF: 0.731 AC: 3530 AN: 4830

European-Finnish (FIN) AF: 0.529 AC: 5592 AN: 10564

Middle Eastern (MID) AF: 0.701 AC: 206 AN: 294

European-Non Finnish (NFE) AF: 0.576 AC: 39177 AN: 67970

Other (OTH) AF: 0.620 AC: 1309 AN: 2112

Alfa AF: 0.567 Hom.: 3051

Bravo AF: 0.597

Asia WGS AF: 0.769 AC: 2672 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.047
DANN	Benign	0.41
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs9387605; hg19: chr6-96063469;