rs4961118

Variant names:

• chr8-89173194-G-T
• rs4961118

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 0.529 in 151,634 control chromosomes in the GnomAD database, including 23,035 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 0.53 (23035 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.517

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.637 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: 0.529 AC: 80167 AN: 151516 Hom.: 23033 Cov.: 32

Gnomad AFR AF: 0.289

Gnomad AMI AF: 0.632

Gnomad AMR AF: 0.611

Gnomad ASJ AF: 0.575

Gnomad EAS AF: 0.578

Gnomad SAS AF: 0.542

Gnomad FIN AF: 0.560

Gnomad MID AF: 0.614

Gnomad NFE AF: 0.642

Gnomad OTH AF: 0.577

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

GnomAD4 genome AF: 0.529 AC: 80198 AN: 151634 Hom.: 23035 Cov.: 32 AF XY: 0.529 AC XY: 39185 AN XY: 74102

Gnomad4 AFR AF: 0.289

Gnomad4 AMR AF: 0.611

Gnomad4 ASJ AF: 0.575

Gnomad4 EAS AF: 0.578

Gnomad4 SAS AF: 0.541

Gnomad4 FIN AF: 0.560

Gnomad4 NFE AF: 0.642

Gnomad4 OTH AF: 0.578

Alfa AF: 0.624 Hom.: 27702

Bravo AF: 0.522

Asia WGS AF: 0.568 AC: 1978 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.40
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4961118; hg19: chr8-90185423;