chr4-141776015-T-G

Variant names:

• chr4-141776015-T-G
• rs6821171

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 0.289 in 152,030 control chromosomes in the GnomAD database, including 6,458 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 (6458 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.535
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.289 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: 0.289 AC: 43951 AN: 151912 Hom.: 6452 Cov.: 32

Gnomad AFR AF: 0.293

Gnomad AMI AF: 0.397

Gnomad AMR AF: 0.248

Gnomad ASJ AF: 0.289

Gnomad EAS AF: 0.243

Gnomad SAS AF: 0.289

Gnomad FIN AF: 0.360

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.289

Gnomad OTH AF: 0.270

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

GnomAD4 genome AF: 0.289 AC: 43973 AN: 152030 Hom.: 6458 Cov.: 32 AF XY: 0.291 AC XY: 21645 AN XY: 74302

African (AFR) AF: 0.293 AC: 12151 AN: 41482

American (AMR) AF: 0.248 AC: 3787 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.289 AC: 1002 AN: 3466

East Asian (EAS) AF: 0.243 AC: 1255 AN: 5160

South Asian (SAS) AF: 0.289 AC: 1392 AN: 4816

European-Finnish (FIN) AF: 0.360 AC: 3791 AN: 10538

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.289 AC: 19620 AN: 67974

Other (OTH) AF: 0.268 AC: 567 AN: 2112

Alfa AF: 0.293 Hom.: 1000

Bravo AF: 0.277

Asia WGS AF: 0.291 AC: 1012 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.23
DANN	Benign	0.49
PhyloP100		-0.54

Splicing

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

Other links and lift over

dbSNP: rs6821171; hg19: chr4-142697168;