rs10514030

Variant names:

• chr18-72087377-T-C
• rs10514030

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 0.0793 in 152,126 control chromosomes in the GnomAD database, including 679 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 0.079 (679 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.401
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.26 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: 0.0793 AC: 12061 AN: 152008 Hom.: 678 Cov.: 32

Gnomad AFR AF: 0.0199

Gnomad AMI AF: 0.121

Gnomad AMR AF: 0.0883

Gnomad ASJ AF: 0.0697

Gnomad EAS AF: 0.273

Gnomad SAS AF: 0.111

Gnomad FIN AF: 0.0771

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0972

Gnomad OTH AF: 0.0746

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

GnomAD4 genome AF: 0.0793 AC: 12056 AN: 152126 Hom.: 679 Cov.: 32 AF XY: 0.0802 AC XY: 5966 AN XY: 74348

African (AFR) AF: 0.0198 AC: 824 AN: 41532

American (AMR) AF: 0.0882 AC: 1344 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.0697 AC: 242 AN: 3470

East Asian (EAS) AF: 0.272 AC: 1404 AN: 5166

South Asian (SAS) AF: 0.111 AC: 536 AN: 4820

European-Finnish (FIN) AF: 0.0771 AC: 817 AN: 10602

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.0972 AC: 6609 AN: 67976

Other (OTH) AF: 0.0738 AC: 156 AN: 2114

Alfa AF: 0.0916 Hom.: 331

Bravo AF: 0.0784

Asia WGS AF: 0.141 AC: 490 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	6.5
DANN	Benign	0.71
PhyloP100		0.40

Splicing

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

Other links and lift over

dbSNP: rs10514030; hg19: chr18-69754612;