rs10738467

Variant names:

• chr9-16910679-C-T
• rs10738467

Variant summary

Our verdict is Benign. The variant received -9 ACMG points: 0P and 9B. BP4 BA1

The variant allele was found at a frequency of 0.411 in 151,946 control chromosomes in the GnomAD database, including 13,951 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 0.41 (13951 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.81
• Publications: 7 publications found

ACMG classification

Our verdict: Benign. The variant received -9 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.14).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.543 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: 0.411 AC: 62351 AN: 151830 Hom.: 13926 Cov.: 32

Gnomad AFR AF: 0.549

Gnomad AMI AF: 0.531

Gnomad AMR AF: 0.530

Gnomad ASJ AF: 0.394

Gnomad EAS AF: 0.291

Gnomad SAS AF: 0.419

Gnomad FIN AF: 0.289

Gnomad MID AF: 0.439

Gnomad NFE AF: 0.326

Gnomad OTH AF: 0.415

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

GnomAD4 genome AF: 0.411 AC: 62427 AN: 151946 Hom.: 13951 Cov.: 32 AF XY: 0.411 AC XY: 30536 AN XY: 74260

African (AFR) AF: 0.549 AC: 22769 AN: 41444

American (AMR) AF: 0.530 AC: 8083 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.394 AC: 1368 AN: 3468

East Asian (EAS) AF: 0.292 AC: 1507 AN: 5162

South Asian (SAS) AF: 0.418 AC: 2013 AN: 4812

European-Finnish (FIN) AF: 0.289 AC: 3055 AN: 10560

Middle Eastern (MID) AF: 0.455 AC: 133 AN: 292

European-Non Finnish (NFE) AF: 0.326 AC: 22139 AN: 67952

Other (OTH) AF: 0.416 AC: 877 AN: 2108

Alfa AF: 0.361 Hom.: 7093

Bravo AF: 0.434

Asia WGS AF: 0.409 AC: 1422 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.14
CADD	Benign	19
DANN	Benign	0.60
PhyloP100		1.8

Splicing

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

Other links and lift over

dbSNP: rs10738467; hg19: chr9-16910677; COSMIC: COSV60335642;