rs9416026

Variant names:

• chr10-72657743-T-C
• rs9416026

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 0.456 in 150,430 control chromosomes in the GnomAD database, including 19,863 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 0.46 (19863 hom., cov: 27)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0790
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.664 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.456 AC: 68561 AN: 150310 Hom.: 19866 Cov.: 27

Gnomad AFR AF: 0.139

Gnomad AMI AF: 0.634

Gnomad AMR AF: 0.458

Gnomad ASJ AF: 0.552

Gnomad EAS AF: 0.0402

Gnomad SAS AF: 0.429

Gnomad FIN AF: 0.480

Gnomad MID AF: 0.587

Gnomad NFE AF: 0.669

Gnomad OTH AF: 0.495

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

GnomAD4 genome AF: 0.456 AC: 68548 AN: 150430 Hom.: 19863 Cov.: 27 AF XY: 0.443 AC XY: 32420 AN XY: 73188

African (AFR) AF: 0.139 AC: 5716 AN: 41172

American (AMR) AF: 0.457 AC: 6853 AN: 14986

Ashkenazi Jewish (ASJ) AF: 0.552 AC: 1912 AN: 3462

East Asian (EAS) AF: 0.0401 AC: 207 AN: 5168

South Asian (SAS) AF: 0.431 AC: 2047 AN: 4750

European-Finnish (FIN) AF: 0.480 AC: 4732 AN: 9864

Middle Eastern (MID) AF: 0.583 AC: 169 AN: 290

European-Non Finnish (NFE) AF: 0.669 AC: 45321 AN: 67750

Other (OTH) AF: 0.488 AC: 1018 AN: 2084

Alfa AF: 0.540 Hom.: 3305

Bravo AF: 0.439

Asia WGS AF: 0.210 AC: 736 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	9.6
DANN	Benign	0.75
PhyloP100		0.079

Splicing

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

Other links and lift over

dbSNP: rs9416026; hg19: chr10-74417501;