rs10514232

chr18-77146580-T-C

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 0.175 in 152,154 control chromosomes in the GnomAD database, including 2,508 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 0.17 (2508 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.782

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.23 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: 0.175 AC: 26562 AN: 152036 Hom.: 2498 Cov.: 33

Gnomad AFR AF: 0.234

Gnomad AMI AF: 0.121

Gnomad AMR AF: 0.160

Gnomad ASJ AF: 0.143

Gnomad EAS AF: 0.0654

Gnomad SAS AF: 0.0874

Gnomad FIN AF: 0.145

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.164

Gnomad OTH AF: 0.165

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

GnomAD4 genome AF: 0.175 AC: 26608 AN: 152154 Hom.: 2508 Cov.: 33 AF XY: 0.173 AC XY: 12844 AN XY: 74390

Gnomad4 AFR AF: 0.234

Gnomad4 AMR AF: 0.160

Gnomad4 ASJ AF: 0.143

Gnomad4 EAS AF: 0.0655

Gnomad4 SAS AF: 0.0867

Gnomad4 FIN AF: 0.145

Gnomad4 NFE AF: 0.164

Gnomad4 OTH AF: 0.172

Alfa AF: 0.162 Hom.: 2693

Bravo AF: 0.175

Asia WGS AF: 0.107 AC: 372 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	3.2
Dann	Benign	0.86

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10514232; hg19: chr18-74858536;