rs4246861

Variant names:

• chr9-25599997-T-C
• rs4246861

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 0.297 in 151,966 control chromosomes in the GnomAD database, including 7,737 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 0.30 (7737 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.515

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.452 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: 0.297 AC: 45116 AN: 151846 Hom.: 7718 Cov.: 32

Gnomad AFR AF: 0.398

Gnomad AMI AF: 0.496

Gnomad AMR AF: 0.461

Gnomad ASJ AF: 0.306

Gnomad EAS AF: 0.426

Gnomad SAS AF: 0.355

Gnomad FIN AF: 0.149

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.204

Gnomad OTH AF: 0.329

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

GnomAD4 genome AF: 0.297 AC: 45168 AN: 151966 Hom.: 7737 Cov.: 32 AF XY: 0.299 AC XY: 22201 AN XY: 74310

Gnomad4 AFR AF: 0.398

Gnomad4 AMR AF: 0.461

Gnomad4 ASJ AF: 0.306

Gnomad4 EAS AF: 0.425

Gnomad4 SAS AF: 0.355

Gnomad4 FIN AF: 0.149

Gnomad4 NFE AF: 0.204

Gnomad4 OTH AF: 0.332

Alfa AF: 0.233 Hom.: 9110

Bravo AF: 0.331

Asia WGS AF: 0.408 AC: 1418 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.58
DANN	Benign	0.27

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4246861; hg19: chr9-25599995;