6-82547829-C-T

Variant names:

• chr6-82547829-C-T
• rs7759870

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 0.451 in 151,430 control chromosomes in the GnomAD database, including 15,413 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 0.45 (15413 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.117
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.47 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: 0.451 AC: 68182 AN: 151312 Hom.: 15398 Cov.: 31

Gnomad AFR AF: 0.455

Gnomad AMI AF: 0.337

Gnomad AMR AF: 0.479

Gnomad ASJ AF: 0.362

Gnomad EAS AF: 0.282

Gnomad SAS AF: 0.330

Gnomad FIN AF: 0.475

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.465

Gnomad OTH AF: 0.460

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

GnomAD4 genome AF: 0.451 AC: 68238 AN: 151430 Hom.: 15413 Cov.: 31 AF XY: 0.447 AC XY: 33066 AN XY: 73986

African (AFR) AF: 0.455 AC: 18789 AN: 41260

American (AMR) AF: 0.479 AC: 7278 AN: 15186

Ashkenazi Jewish (ASJ) AF: 0.362 AC: 1251 AN: 3456

East Asian (EAS) AF: 0.281 AC: 1441 AN: 5122

South Asian (SAS) AF: 0.328 AC: 1580 AN: 4820

European-Finnish (FIN) AF: 0.475 AC: 4973 AN: 10470

Middle Eastern (MID) AF: 0.391 AC: 115 AN: 294

European-Non Finnish (NFE) AF: 0.465 AC: 31540 AN: 67810

Other (OTH) AF: 0.459 AC: 964 AN: 2102

Alfa AF: 0.443 Hom.: 1883

Bravo AF: 0.454

Asia WGS AF: 0.307 AC: 1066 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	3.7
DANN	Benign	0.41
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs7759870; hg19: chr6-83257546; COSMIC: COSV69409546;