10-18139486-C-T

Variant names:

• chr10-18139486-C-T
• rs10764319

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 0.343 in 152,070 control chromosomes in the GnomAD database, including 9,223 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 0.34 (9223 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0730
• Publications: 3 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 = 0.441 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.343 AC: 52110 AN: 151952 Hom.: 9200 Cov.: 33

Gnomad AFR AF: 0.401

Gnomad AMI AF: 0.207

Gnomad AMR AF: 0.261

Gnomad ASJ AF: 0.307

Gnomad EAS AF: 0.458

Gnomad SAS AF: 0.336

Gnomad FIN AF: 0.424

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.310

Gnomad OTH AF: 0.304

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

GnomAD4 genome AF: 0.343 AC: 52173 AN: 152070 Hom.: 9223 Cov.: 33 AF XY: 0.347 AC XY: 25765 AN XY: 74322

African (AFR) AF: 0.401 AC: 16652 AN: 41486

American (AMR) AF: 0.261 AC: 3997 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.307 AC: 1065 AN: 3470

East Asian (EAS) AF: 0.456 AC: 2350 AN: 5148

South Asian (SAS) AF: 0.335 AC: 1618 AN: 4826

European-Finnish (FIN) AF: 0.424 AC: 4482 AN: 10576

Middle Eastern (MID) AF: 0.238 AC: 70 AN: 294

European-Non Finnish (NFE) AF: 0.310 AC: 21092 AN: 67956

Other (OTH) AF: 0.312 AC: 658 AN: 2112

Alfa AF: 0.300 Hom.: 8793

Bravo AF: 0.331

Asia WGS AF: 0.383 AC: 1330 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.7
DANN	Benign	0.38
PhyloP100		-0.073

Splicing

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

Other links and lift over

dbSNP: rs10764319; hg19: chr10-18428415;