rs4744106

Variant names:

• chr9-90111383-G-A
• rs4744106

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 0.493 in 152,012 control chromosomes in the GnomAD database, including 18,863 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 0.49 (18863 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.979
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.582 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: 0.493 AC: 74936 AN: 151894 Hom.: 18853 Cov.: 33

Gnomad AFR AF: 0.405

Gnomad AMI AF: 0.649

Gnomad AMR AF: 0.592

Gnomad ASJ AF: 0.404

Gnomad EAS AF: 0.430

Gnomad SAS AF: 0.416

Gnomad FIN AF: 0.533

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.532

Gnomad OTH AF: 0.495

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

GnomAD4 genome AF: 0.493 AC: 74985 AN: 152012 Hom.: 18863 Cov.: 33 AF XY: 0.494 AC XY: 36674 AN XY: 74294

African (AFR) AF: 0.405 AC: 16783 AN: 41430

American (AMR) AF: 0.592 AC: 9058 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.404 AC: 1400 AN: 3468

East Asian (EAS) AF: 0.430 AC: 2220 AN: 5164

South Asian (SAS) AF: 0.417 AC: 2013 AN: 4824

European-Finnish (FIN) AF: 0.533 AC: 5623 AN: 10554

Middle Eastern (MID) AF: 0.466 AC: 136 AN: 292

European-Non Finnish (NFE) AF: 0.532 AC: 36131 AN: 67970

Other (OTH) AF: 0.489 AC: 1032 AN: 2112

Alfa AF: 0.518 Hom.: 40973

Bravo AF: 0.499

Asia WGS AF: 0.421 AC: 1464 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.5
DANN	Benign	0.77
PhyloP100		-0.98

Splicing

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

Other links and lift over

dbSNP: rs4744106; hg19: chr9-92873665;