6-82570340-T-G

Variant names:

• chr6-82570340-T-G
• rs2917494

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 0.204 in 152,064 control chromosomes in the GnomAD database, including 3,311 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 0.20 (3311 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00200
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.301 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: 0.204 AC: 31003 AN: 151944 Hom.: 3301 Cov.: 32

Gnomad AFR AF: 0.175

Gnomad AMI AF: 0.147

Gnomad AMR AF: 0.307

Gnomad ASJ AF: 0.213

Gnomad EAS AF: 0.197

Gnomad SAS AF: 0.189

Gnomad FIN AF: 0.202

Gnomad MID AF: 0.159

Gnomad NFE AF: 0.201

Gnomad OTH AF: 0.220

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

GnomAD4 genome AF: 0.204 AC: 31021 AN: 152064 Hom.: 3311 Cov.: 32 AF XY: 0.207 AC XY: 15363 AN XY: 74298

African (AFR) AF: 0.175 AC: 7254 AN: 41522

American (AMR) AF: 0.308 AC: 4692 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.213 AC: 738 AN: 3472

East Asian (EAS) AF: 0.196 AC: 1013 AN: 5162

South Asian (SAS) AF: 0.187 AC: 899 AN: 4806

European-Finnish (FIN) AF: 0.202 AC: 2135 AN: 10562

Middle Eastern (MID) AF: 0.154 AC: 45 AN: 292

European-Non Finnish (NFE) AF: 0.201 AC: 13651 AN: 67986

Other (OTH) AF: 0.218 AC: 460 AN: 2110

Alfa AF: 0.175 Hom.: 930

Bravo AF: 0.216

Asia WGS AF: 0.186 AC: 648 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	5.0
DANN	Benign	0.67
PhyloP100		-0.0020

Splicing

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

Other links and lift over

dbSNP: rs2917494; hg19: chr6-83280057;