6-50987368-C-T

Variant names:

• chr6-50987368-C-T
• rs11759809

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 0.285 in 152,012 control chromosomes in the GnomAD database, including 6,629 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 0.29 (6629 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.776
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.69).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.339 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: 0.286 AC: 43368 AN: 151894 Hom.: 6632 Cov.: 32

Gnomad AFR AF: 0.186

Gnomad AMI AF: 0.202

Gnomad AMR AF: 0.347

Gnomad ASJ AF: 0.250

Gnomad EAS AF: 0.219

Gnomad SAS AF: 0.314

Gnomad FIN AF: 0.286

Gnomad MID AF: 0.207

Gnomad NFE AF: 0.339

Gnomad OTH AF: 0.267

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

GnomAD4 genome AF: 0.285 AC: 43379 AN: 152012 Hom.: 6629 Cov.: 32 AF XY: 0.283 AC XY: 20988 AN XY: 74286

African (AFR) AF: 0.186 AC: 7704 AN: 41516

American (AMR) AF: 0.347 AC: 5291 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.250 AC: 865 AN: 3466

East Asian (EAS) AF: 0.218 AC: 1122 AN: 5140

South Asian (SAS) AF: 0.314 AC: 1510 AN: 4812

European-Finnish (FIN) AF: 0.286 AC: 3020 AN: 10566

Middle Eastern (MID) AF: 0.205 AC: 60 AN: 292

European-Non Finnish (NFE) AF: 0.339 AC: 23066 AN: 67950

Other (OTH) AF: 0.264 AC: 557 AN: 2112

Alfa AF: 0.321 Hom.: 11298

Bravo AF: 0.286

Asia WGS AF: 0.294 AC: 1024 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
CADD	Benign	1.4
DANN	Benign	0.81
PhyloP100		-0.78

Splicing

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

Other links and lift over

dbSNP: rs11759809; hg19: chr6-50955081;