rs9461045

Variant names:

• chr6-24648833-C-T
• rs9461045

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 0.221 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
• Publications: 38 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.201 AC: 8097 AN: 40352

American (AMR) AF: 0.362 AC: 5340 AN: 14768

Ashkenazi Jewish (ASJ) AF: 0.209 AC: 722 AN: 3450

East Asian (EAS) AF: 0.629 AC: 3079 AN: 4892

South Asian (SAS) AF: 0.421 AC: 1955 AN: 4642

European-Finnish (FIN) AF: 0.116 AC: 1172 AN: 10146

Middle Eastern (MID) AF: 0.331 AC: 96 AN: 290

European-Non Finnish (NFE) AF: 0.172 AC: 11588 AN: 67298

Other (OTH) AF: 0.237 AC: 487 AN: 2058

Alfa AF: 0.202 Hom.: 5843

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
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs9461045; hg19: chr6-24649061;