rs4460498

Variant names:

• chr9-97858130-T-C
• rs4460498

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.635 in 151,936 control chromosomes in the GnomAD database, including 30,879 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 0.63 (30879 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.36
• Publications: 21 publications found

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.37).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.864 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: 0.635 AC: 96358 AN: 151816 Hom.: 30852 Cov.: 31

Gnomad AFR AF: 0.665

Gnomad AMI AF: 0.415

Gnomad AMR AF: 0.651

Gnomad ASJ AF: 0.477

Gnomad EAS AF: 0.885

Gnomad SAS AF: 0.634

Gnomad FIN AF: 0.645

Gnomad MID AF: 0.615

Gnomad NFE AF: 0.603

Gnomad OTH AF: 0.628

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

GnomAD4 genome AF: 0.635 AC: 96423 AN: 151936 Hom.: 30879 Cov.: 31 AF XY: 0.639 AC XY: 47470 AN XY: 74268

African (AFR) AF: 0.665 AC: 27553 AN: 41446

American (AMR) AF: 0.651 AC: 9949 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.477 AC: 1653 AN: 3466

East Asian (EAS) AF: 0.885 AC: 4564 AN: 5156

South Asian (SAS) AF: 0.633 AC: 3041 AN: 4804

European-Finnish (FIN) AF: 0.645 AC: 6809 AN: 10550

Middle Eastern (MID) AF: 0.617 AC: 179 AN: 290

European-Non Finnish (NFE) AF: 0.603 AC: 40971 AN: 67922

Other (OTH) AF: 0.627 AC: 1326 AN: 2114

Alfa AF: 0.626 Hom.: 6079

Bravo AF: 0.638

Asia WGS AF: 0.718 AC: 2501 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.37
CADD	Benign	17
DANN	Benign	0.60
PhyloP100		2.4

Splicing

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

Other links and lift over

dbSNP: rs4460498; hg19: chr9-100620412;