rs10514232

Variant names:

• chr18-77146580-T-C
• rs10514232

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 0.175 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
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.234 AC: 9694 AN: 41488

American (AMR) AF: 0.160 AC: 2443 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.143 AC: 496 AN: 3466

East Asian (EAS) AF: 0.0655 AC: 339 AN: 5172

South Asian (SAS) AF: 0.0867 AC: 418 AN: 4824

European-Finnish (FIN) AF: 0.145 AC: 1540 AN: 10604

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.164 AC: 11184 AN: 67990

Other (OTH) AF: 0.172 AC: 363 AN: 2114

Alfa AF: 0.164 Hom.: 3485

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
PhyloP100		-0.78

Splicing

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

Other links and lift over

dbSNP: rs10514232; hg19: chr18-74858536;