rs10503049

Positions:

• chr18-61066081-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.0187 in 150,210 control chromosomes in the GnomAD database, including 46 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 0.019 (46 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.01

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BS1: Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.0187 (2814/150210) while in subpopulation SAS AF= 0.0544 (259/4764). AF 95% confidence interval is 0.0489. There are 46 homozygotes in gnomad4. There are 1420 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 46 gene

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: 0.0186 AC: 2794 AN: 150120 Hom.: 42 Cov.: 32

Gnomad AFR AF: 0.0270

Gnomad AMI AF: 0.00549

Gnomad AMR AF: 0.0132

Gnomad ASJ AF: 0.0203

Gnomad EAS AF: 0.0456

Gnomad SAS AF: 0.0541

Gnomad FIN AF: 0.00249

Gnomad MID AF: 0.0223

Gnomad NFE AF: 0.0127

Gnomad OTH AF: 0.0208

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

GnomAD4 genome AF: 0.0187 AC: 2814 AN: 150210 Hom.: 46 Cov.: 32 AF XY: 0.0194 AC XY: 1420 AN XY: 73268

Gnomad4 AFR AF: 0.0273

Gnomad4 AMR AF: 0.0132

Gnomad4 ASJ AF: 0.0203

Gnomad4 EAS AF: 0.0457

Gnomad4 SAS AF: 0.0544

Gnomad4 FIN AF: 0.00249

Gnomad4 NFE AF: 0.0127

Gnomad4 OTH AF: 0.0230

Alfa AF: 0.0126 Hom.: 4

Bravo AF: 0.0199

Asia WGS AF: 0.0440 AC: 152 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.10
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10503049; hg19: chr18-58733314;