rs10140345

chr14-97164530-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.473 in 152,018 control chromosomes in the GnomAD database, including 17,360 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 0.47 (17360 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0770

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.49).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.508 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.473 AC: 71832 AN: 151900 Hom.: 17338 Cov.: 32

Gnomad AFR AF: 0.482

Gnomad AMI AF: 0.568

Gnomad AMR AF: 0.409

Gnomad ASJ AF: 0.474

Gnomad EAS AF: 0.339

Gnomad SAS AF: 0.382

Gnomad FIN AF: 0.375

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.512

Gnomad OTH AF: 0.473

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

GnomAD4 genome AF: 0.473 AC: 71905 AN: 152018 Hom.: 17360 Cov.: 32 AF XY: 0.461 AC XY: 34248 AN XY: 74296

Gnomad4 AFR AF: 0.483

Gnomad4 AMR AF: 0.408

Gnomad4 ASJ AF: 0.474

Gnomad4 EAS AF: 0.340

Gnomad4 SAS AF: 0.383

Gnomad4 FIN AF: 0.375

Gnomad4 NFE AF: 0.512

Gnomad4 OTH AF: 0.473

Alfa AF: 0.488 Hom.: 2276

Bravo AF: 0.477

Asia WGS AF: 0.391 AC: 1355 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.49
Cadd	Benign	12
Dann	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10140345; hg19: chr14-97630867;