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. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.954

Gnomad4 AMR AF: 0.911

Gnomad4 ASJ AF: 0.887

Gnomad4 EAS AF: 0.853

Gnomad4 SAS AF: 0.882

Gnomad4 FIN AF: 0.856

Gnomad4 NFE AF: 0.912

Gnomad4 OTH AF: 0.901

Alfa AF: 0.918 Hom.: 17026

Bravo AF: 0.922

Asia WGS AF: 0.875 AC: 3046 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4877149; hg19: chr9-82343802;