rs871153

Variant names:

• chr4-102095721-G-T
• rs871153

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 0.288 in 152,110 control chromosomes in the GnomAD database, including 7,766 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 (7766 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.530
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.421 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: 0.288 AC: 43842 AN: 151992 Hom.: 7769 Cov.: 32

Gnomad AFR AF: 0.0820

Gnomad AMI AF: 0.473

Gnomad AMR AF: 0.299

Gnomad ASJ AF: 0.361

Gnomad EAS AF: 0.276

Gnomad SAS AF: 0.437

Gnomad FIN AF: 0.288

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.395

Gnomad OTH AF: 0.328

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

GnomAD4 genome AF: 0.288 AC: 43835 AN: 152110 Hom.: 7766 Cov.: 32 AF XY: 0.284 AC XY: 21080 AN XY: 74350

African (AFR) AF: 0.0818 AC: 3396 AN: 41524

American (AMR) AF: 0.299 AC: 4569 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.361 AC: 1253 AN: 3472

East Asian (EAS) AF: 0.276 AC: 1422 AN: 5156

South Asian (SAS) AF: 0.437 AC: 2104 AN: 4820

European-Finnish (FIN) AF: 0.288 AC: 3038 AN: 10562

Middle Eastern (MID) AF: 0.364 AC: 107 AN: 294

European-Non Finnish (NFE) AF: 0.395 AC: 26827 AN: 67982

Other (OTH) AF: 0.327 AC: 689 AN: 2108

Alfa AF: 0.373 Hom.: 5833

Bravo AF: 0.277

Asia WGS AF: 0.323 AC: 1124 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	0.62
DANN	Benign	0.85
PhyloP100		-0.53

Splicing

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

Other links and lift over

dbSNP: rs871153; hg19: chr4-103016878;