rs4871877

Variant names:

• chr8-23514627-T-A
• rs4871877

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 0.309 in 152,206 control chromosomes in the GnomAD database, including 7,352 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 0.31 (7352 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.31
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.461 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: 0.309 AC: 46933 AN: 152088 Hom.: 7347 Cov.: 33

Gnomad AFR AF: 0.303

Gnomad AMI AF: 0.290

Gnomad AMR AF: 0.268

Gnomad ASJ AF: 0.248

Gnomad EAS AF: 0.476

Gnomad SAS AF: 0.377

Gnomad FIN AF: 0.263

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.314

Gnomad OTH AF: 0.304

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

GnomAD4 genome AF: 0.309 AC: 46967 AN: 152206 Hom.: 7352 Cov.: 33 AF XY: 0.305 AC XY: 22720 AN XY: 74408

African (AFR) AF: 0.303 AC: 12570 AN: 41504

American (AMR) AF: 0.268 AC: 4106 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.248 AC: 862 AN: 3472

East Asian (EAS) AF: 0.476 AC: 2468 AN: 5182

South Asian (SAS) AF: 0.378 AC: 1824 AN: 4824

European-Finnish (FIN) AF: 0.263 AC: 2786 AN: 10592

Middle Eastern (MID) AF: 0.330 AC: 97 AN: 294

European-Non Finnish (NFE) AF: 0.314 AC: 21339 AN: 68014

Other (OTH) AF: 0.308 AC: 651 AN: 2116

Alfa AF: 0.304 Hom.: 874

Bravo AF: 0.308

Asia WGS AF: 0.399 AC: 1387 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	9.9
DANN	Benign	0.81
PhyloP100		2.3

Splicing

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

Other links and lift over

dbSNP: rs4871877; hg19: chr8-23372140;