rs10503049

Variant names:

• chr18-61066081-C-T
• rs10503049

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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 the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 46 gene

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: 0.0186 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

African (AFR) AF: 0.0273 AC: 1112 AN: 40784

American (AMR) AF: 0.0132 AC: 199 AN: 15062

Ashkenazi Jewish (ASJ) AF: 0.0203 AC: 70 AN: 3452

East Asian (EAS) AF: 0.0457 AC: 233 AN: 5100

South Asian (SAS) AF: 0.0544 AC: 259 AN: 4764

European-Finnish (FIN) AF: 0.00249 AC: 25 AN: 10060

Middle Eastern (MID) AF: 0.0207 AC: 6 AN: 290

European-Non Finnish (NFE) AF: 0.0127 AC: 857 AN: 67702

Other (OTH) AF: 0.0230 AC: 48 AN: 2086

Alfa AF: 0.0184 Hom.: 13

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
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs10503049; hg19: chr18-58733314;