4-89863377-A-G

Variant names:

• chr4-89863377-A-G
• rs2736994

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 0.786 in 151,934 control chromosomes in the GnomAD database, including 47,032 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 0.79 (47032 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.338

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.795 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: 0.786 AC: 119290 AN: 151816 Hom.: 46985 Cov.: 30

Gnomad AFR AF: 0.802

Gnomad AMI AF: 0.820

Gnomad AMR AF: 0.741

Gnomad ASJ AF: 0.710

Gnomad EAS AF: 0.776

Gnomad SAS AF: 0.661

Gnomad FIN AF: 0.830

Gnomad MID AF: 0.704

Gnomad NFE AF: 0.792

Gnomad OTH AF: 0.782

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

GnomAD4 genome AF: 0.786 AC: 119387 AN: 151934 Hom.: 47032 Cov.: 30 AF XY: 0.783 AC XY: 58096 AN XY: 74236

Gnomad4 AFR AF: 0.802

Gnomad4 AMR AF: 0.741

Gnomad4 ASJ AF: 0.710

Gnomad4 EAS AF: 0.776

Gnomad4 SAS AF: 0.662

Gnomad4 FIN AF: 0.830

Gnomad4 NFE AF: 0.792

Gnomad4 OTH AF: 0.776

Alfa AF: 0.788 Hom.: 10500

Bravo AF: 0.785

Asia WGS AF: 0.725 AC: 2522 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	5.5
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2736994; hg19: chr4-90784528;