rs10468473

Variant names:

• chr17-12224359-T-C
• rs10468473

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 0.0913 in 152,196 control chromosomes in the GnomAD database, including 803 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 0.091 (803 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.126
• Publications: 7 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.278 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: 0.0914 AC: 13905 AN: 152078 Hom.: 804 Cov.: 32

Gnomad AFR AF: 0.0563

Gnomad AMI AF: 0.131

Gnomad AMR AF: 0.0870

Gnomad ASJ AF: 0.0562

Gnomad EAS AF: 0.290

Gnomad SAS AF: 0.144

Gnomad FIN AF: 0.0903

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0968

Gnomad OTH AF: 0.0837

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

GnomAD4 genome AF: 0.0913 AC: 13896 AN: 152196 Hom.: 803 Cov.: 32 AF XY: 0.0933 AC XY: 6944 AN XY: 74406

African (AFR) AF: 0.0561 AC: 2330 AN: 41526

American (AMR) AF: 0.0871 AC: 1332 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0562 AC: 195 AN: 3468

East Asian (EAS) AF: 0.290 AC: 1495 AN: 5160

South Asian (SAS) AF: 0.144 AC: 694 AN: 4824

European-Finnish (FIN) AF: 0.0903 AC: 958 AN: 10604

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.0968 AC: 6585 AN: 68004

Other (OTH) AF: 0.0824 AC: 174 AN: 2112

Alfa AF: 0.0946 Hom.: 2610

Bravo AF: 0.0903

Asia WGS AF: 0.214 AC: 744 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.9
DANN	Benign	0.55
PhyloP100		-0.13

Splicing

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

Other links and lift over

dbSNP: rs10468473; hg19: chr17-12127676;