rs4877149

chr9-79728887-G-Achr9-79728887-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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;