6-50974837-T-G

Variant names:

• chr6-50974837-T-G
• rs10484665

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 0.254 in 152,008 control chromosomes in the GnomAD database, including 5,228 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 0.25 (5228 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.227
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.332 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.254 AC: 38635 AN: 151890 Hom.: 5231 Cov.: 32

Gnomad AFR AF: 0.183

Gnomad AMI AF: 0.155

Gnomad AMR AF: 0.340

Gnomad ASJ AF: 0.230

Gnomad EAS AF: 0.228

Gnomad SAS AF: 0.312

Gnomad FIN AF: 0.250

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.281

Gnomad OTH AF: 0.247

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

GnomAD4 genome AF: 0.254 AC: 38643 AN: 152008 Hom.: 5228 Cov.: 32 AF XY: 0.254 AC XY: 18836 AN XY: 74296

African (AFR) AF: 0.182 AC: 7566 AN: 41464

American (AMR) AF: 0.340 AC: 5189 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.230 AC: 797 AN: 3472

East Asian (EAS) AF: 0.227 AC: 1173 AN: 5164

South Asian (SAS) AF: 0.313 AC: 1504 AN: 4812

European-Finnish (FIN) AF: 0.250 AC: 2639 AN: 10548

Middle Eastern (MID) AF: 0.201 AC: 59 AN: 294

European-Non Finnish (NFE) AF: 0.280 AC: 19060 AN: 67952

Other (OTH) AF: 0.244 AC: 515 AN: 2110

Alfa AF: 0.259 Hom.: 4150

Bravo AF: 0.258

Asia WGS AF: 0.291 AC: 1013 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.0
DANN	Benign	0.79
PhyloP100		-0.23

Splicing

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

Other links and lift over

dbSNP: rs10484665; hg19: chr6-50942550;