rs489095

Variant names:

• chr5-4923516-A-G
• rs489095

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 0.484 in 152,184 control chromosomes in the GnomAD database, including 21,243 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 0.48 (21243 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.186
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.652 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: 0.484 AC: 73629 AN: 152066 Hom.: 21247 Cov.: 33

Gnomad AFR AF: 0.208

Gnomad AMI AF: 0.731

Gnomad AMR AF: 0.525

Gnomad ASJ AF: 0.526

Gnomad EAS AF: 0.0104

Gnomad SAS AF: 0.439

Gnomad FIN AF: 0.612

Gnomad MID AF: 0.491

Gnomad NFE AF: 0.657

Gnomad OTH AF: 0.490

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

GnomAD4 genome AF: 0.484 AC: 73641 AN: 152184 Hom.: 21243 Cov.: 33 AF XY: 0.479 AC XY: 35645 AN XY: 74400

African (AFR) AF: 0.208 AC: 8622 AN: 41536

American (AMR) AF: 0.525 AC: 8027 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.526 AC: 1827 AN: 3472

East Asian (EAS) AF: 0.0104 AC: 54 AN: 5176

South Asian (SAS) AF: 0.439 AC: 2114 AN: 4816

European-Finnish (FIN) AF: 0.612 AC: 6471 AN: 10580

Middle Eastern (MID) AF: 0.493 AC: 145 AN: 294

European-Non Finnish (NFE) AF: 0.657 AC: 44693 AN: 67994

Other (OTH) AF: 0.484 AC: 1023 AN: 2114

Alfa AF: 0.552 Hom.: 4403

Bravo AF: 0.460

Asia WGS AF: 0.213 AC: 741 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	1.0
DANN	Benign	0.80
PhyloP100		-0.19

Splicing

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

Other links and lift over

dbSNP: rs489095; hg19: chr5-4923629;