chr10-120158547-C-T

Variant names:

• chr10-120158547-C-T
• rs1537219

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 0.536 in 151,966 control chromosomes in the GnomAD database, including 22,417 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 0.54 (22417 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.487
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.62).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.708 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: 0.536 AC: 81343 AN: 151846 Hom.: 22407 Cov.: 32

Gnomad AFR AF: 0.414

Gnomad AMI AF: 0.530

Gnomad AMR AF: 0.643

Gnomad ASJ AF: 0.556

Gnomad EAS AF: 0.728

Gnomad SAS AF: 0.478

Gnomad FIN AF: 0.689

Gnomad MID AF: 0.541

Gnomad NFE AF: 0.549

Gnomad OTH AF: 0.557

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

GnomAD4 genome AF: 0.536 AC: 81393 AN: 151966 Hom.: 22417 Cov.: 32 AF XY: 0.544 AC XY: 40390 AN XY: 74246

African (AFR) AF: 0.414 AC: 17148 AN: 41412

American (AMR) AF: 0.644 AC: 9836 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.556 AC: 1930 AN: 3472

East Asian (EAS) AF: 0.728 AC: 3760 AN: 5166

South Asian (SAS) AF: 0.477 AC: 2294 AN: 4806

European-Finnish (FIN) AF: 0.689 AC: 7277 AN: 10560

Middle Eastern (MID) AF: 0.562 AC: 164 AN: 292

European-Non Finnish (NFE) AF: 0.549 AC: 37321 AN: 67958

Other (OTH) AF: 0.560 AC: 1183 AN: 2114

Alfa AF: 0.486 Hom.: 2364

Bravo AF: 0.528

Asia WGS AF: 0.583 AC: 2028 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.62
CADD	Benign	15
DANN	Benign	0.83
PhyloP100		0.49

Splicing

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

Other links and lift over

dbSNP: rs1537219; hg19: chr10-121918059;