chr6-95827662-G-A

Variant names:

• chr6-95827662-G-A
• rs6899560

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 0.932 in 152,280 control chromosomes in the GnomAD database, including 66,214 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 0.93 (66214 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.41
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.09).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 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: 0.932 AC: 141790 AN: 152162 Hom.: 66165 Cov.: 32

Gnomad AFR AF: 0.878

Gnomad AMI AF: 0.963

Gnomad AMR AF: 0.945

Gnomad ASJ AF: 0.958

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.993

Gnomad FIN AF: 0.971

Gnomad MID AF: 0.971

Gnomad NFE AF: 0.944

Gnomad OTH AF: 0.932

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

GnomAD4 genome AF: 0.932 AC: 141897 AN: 152280 Hom.: 66214 Cov.: 32 AF XY: 0.936 AC XY: 69677 AN XY: 74468

African (AFR) AF: 0.878 AC: 36470 AN: 41542

American (AMR) AF: 0.945 AC: 14453 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.958 AC: 3325 AN: 3472

East Asian (EAS) AF: 1.00 AC: 5173 AN: 5174

South Asian (SAS) AF: 0.992 AC: 4793 AN: 4830

European-Finnish (FIN) AF: 0.971 AC: 10322 AN: 10626

Middle Eastern (MID) AF: 0.973 AC: 284 AN: 292

European-Non Finnish (NFE) AF: 0.944 AC: 64228 AN: 68030

Other (OTH) AF: 0.932 AC: 1971 AN: 2114

Alfa AF: 0.942 Hom.: 141129

Bravo AF: 0.927

Asia WGS AF: 0.986 AC: 3429 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.26
DANN	Benign	0.14
PhyloP100		-2.4

Splicing

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

Other links and lift over

dbSNP: rs6899560; hg19: chr6-96275538;