rs10514168

chr18-75386994-C-A

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 0.128 in 152,296 control chromosomes in the GnomAD database, including 1,394 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 0.13 (1394 hom., cov: 33)
  • Exomes 𝑓: 0.14 (0 hom.)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.813

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.69).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.158 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: 0.128 AC: 19520 AN: 152158 Hom.: 1391 Cov.: 33

Gnomad AFR AF: 0.0721

Gnomad AMI AF: 0.250

Gnomad AMR AF: 0.162

Gnomad ASJ AF: 0.0893

Gnomad EAS AF: 0.00788

Gnomad SAS AF: 0.105

Gnomad FIN AF: 0.162

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.161

Gnomad OTH AF: 0.125

GnomAD4 exome AF: 0.136 AC: 3 AN: 22 Hom.: 0 AF XY: 0.125 AC XY: 2 AN XY: 16

Gnomad4 FIN exome AF: 0.100

Gnomad4 NFE exome AF: 0.200

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.128 AC: 19547 AN: 152274 Hom.: 1394 Cov.: 33 AF XY: 0.125 AC XY: 9316 AN XY: 74464

Gnomad4 AFR AF: 0.0722

Gnomad4 AMR AF: 0.163

Gnomad4 ASJ AF: 0.0893

Gnomad4 EAS AF: 0.00790

Gnomad4 SAS AF: 0.106

Gnomad4 FIN AF: 0.162

Gnomad4 NFE AF: 0.161

Gnomad4 OTH AF: 0.124

Alfa AF: 0.143 Hom.: 223

Bravo AF: 0.129

Asia WGS AF: 0.0730 AC: 252 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
Cadd	Benign	4.1
Dann	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10514168; hg19: chr18-73098949;