rs9461045

chr6-24648833-C-T

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 0.221 in 148,784 control chromosomes in the GnomAD database, including 4,599 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 0.22 (4599 hom., cov: 25)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.90

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.611 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: 0.221 AC: 32831 AN: 148666 Hom.: 4598 Cov.: 25

Gnomad AFR AF: 0.201

Gnomad AMI AF: 0.355

Gnomad AMR AF: 0.361

Gnomad ASJ AF: 0.209

Gnomad EAS AF: 0.629

Gnomad SAS AF: 0.423

Gnomad FIN AF: 0.116

Gnomad MID AF: 0.321

Gnomad NFE AF: 0.172

Gnomad OTH AF: 0.235

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

GnomAD4 genome AF: 0.221 AC: 32851 AN: 148784 Hom.: 4599 Cov.: 25 AF XY: 0.226 AC XY: 16375 AN XY: 72512

Gnomad4 AFR AF: 0.201

Gnomad4 AMR AF: 0.362

Gnomad4 ASJ AF: 0.209

Gnomad4 EAS AF: 0.629

Gnomad4 SAS AF: 0.421

Gnomad4 FIN AF: 0.116

Gnomad4 NFE AF: 0.172

Gnomad4 OTH AF: 0.237

Alfa AF: 0.199 Hom.: 4487

Bravo AF: 0.240

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	0.38
Dann	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9461045; hg19: chr6-24649061;