rs4877149

Variant names:

• chr9-79728887-G-A
• rs4877149

Your query was ambiguous. Multiple possible variants found:

• chr9-79728887-G-A
• chr9-79728887-G-T

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 0.916 in 152,208 control chromosomes in the GnomAD database, including 63,922 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 0.92 (63922 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.235
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.946 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: 0.916 AC: 139289 AN: 152090 Hom.: 63855 Cov.: 31

Gnomad AFR AF: 0.954

Gnomad AMI AF: 0.961

Gnomad AMR AF: 0.911

Gnomad ASJ AF: 0.887

Gnomad EAS AF: 0.854

Gnomad SAS AF: 0.881

Gnomad FIN AF: 0.856

Gnomad MID AF: 0.934

Gnomad NFE AF: 0.912

Gnomad OTH AF: 0.900

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

GnomAD4 genome AF: 0.916 AC: 139416 AN: 152208 Hom.: 63922 Cov.: 31 AF XY: 0.911 AC XY: 67805 AN XY: 74402

African (AFR) AF: 0.954 AC: 39604 AN: 41526

American (AMR) AF: 0.911 AC: 13932 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.887 AC: 3078 AN: 3472

East Asian (EAS) AF: 0.853 AC: 4412 AN: 5170

South Asian (SAS) AF: 0.882 AC: 4250 AN: 4820

European-Finnish (FIN) AF: 0.856 AC: 9060 AN: 10588

Middle Eastern (MID) AF: 0.932 AC: 274 AN: 294

European-Non Finnish (NFE) AF: 0.912 AC: 62025 AN: 68024

Other (OTH) AF: 0.901 AC: 1905 AN: 2114

Alfa AF: 0.916 Hom.: 26144

Bravo AF: 0.922

Asia WGS AF: 0.875 AC: 3046 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.0
DANN	Benign	0.44
PhyloP100		0.23

Splicing

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

Other links and lift over

dbSNP: rs4877149; hg19: chr9-82343802;