rs4460498

chr9-97858130-T-C

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.665

Gnomad4 AMR AF: 0.651

Gnomad4 ASJ AF: 0.477

Gnomad4 EAS AF: 0.885

Gnomad4 SAS AF: 0.633

Gnomad4 FIN AF: 0.645

Gnomad4 NFE AF: 0.603

Gnomad4 OTH AF: 0.627

Alfa AF: 0.627 Hom.: 5157

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4460498; hg19: chr9-100620412;