6-36584490-C-G

Variant names:

• chr6-36584490-C-G
• rs7759778

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 0.244 in 151,202 control chromosomes in the GnomAD database, including 4,676 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 0.24 (4676 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.777
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.374 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: 0.244 AC: 36803 AN: 151130 Hom.: 4673 Cov.: 31

Gnomad AFR AF: 0.203

Gnomad AMI AF: 0.300

Gnomad AMR AF: 0.215

Gnomad ASJ AF: 0.230

Gnomad EAS AF: 0.388

Gnomad SAS AF: 0.227

Gnomad FIN AF: 0.326

Gnomad MID AF: 0.175

Gnomad NFE AF: 0.253

Gnomad OTH AF: 0.232

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

GnomAD4 genome AF: 0.244 AC: 36832 AN: 151202 Hom.: 4676 Cov.: 31 AF XY: 0.246 AC XY: 18132 AN XY: 73776

African (AFR) AF: 0.203 AC: 8399 AN: 41288

American (AMR) AF: 0.215 AC: 3250 AN: 15144

Ashkenazi Jewish (ASJ) AF: 0.230 AC: 797 AN: 3468

East Asian (EAS) AF: 0.388 AC: 1999 AN: 5148

South Asian (SAS) AF: 0.228 AC: 1092 AN: 4794

European-Finnish (FIN) AF: 0.326 AC: 3331 AN: 10228

Middle Eastern (MID) AF: 0.167 AC: 48 AN: 288

European-Non Finnish (NFE) AF: 0.253 AC: 17152 AN: 67842

Other (OTH) AF: 0.235 AC: 492 AN: 2096

Alfa AF: 0.240 Hom.: 577

Bravo AF: 0.235

Asia WGS AF: 0.275 AC: 956 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.8
DANN	Benign	0.58
PhyloP100		0.78

Splicing

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

Other links and lift over

dbSNP: rs7759778; hg19: chr6-36552267;