chr18-61243948-G-A

Variant names:

• chr18-61243948-G-A
• rs10503053

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.00894 in 151,980 control chromosomes in the GnomAD database, including 20 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 0.0089 (20 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.149
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.32).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0611 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: 0.00899 AC: 1366 AN: 151872 Hom.: 20 Cov.: 32

Gnomad AFR AF: 0.00232

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0184

Gnomad ASJ AF: 0.00346

Gnomad EAS AF: 0.0671

Gnomad SAS AF: 0.0222

Gnomad FIN AF: 0.00361

Gnomad MID AF: 0.00641

Gnomad NFE AF: 0.00688

Gnomad OTH AF: 0.00766

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

GnomAD4 genome AF: 0.00894 AC: 1359 AN: 151980 Hom.: 20 Cov.: 32 AF XY: 0.00956 AC XY: 710 AN XY: 74268

African (AFR) AF: 0.00231 AC: 96 AN: 41474

American (AMR) AF: 0.0183 AC: 279 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.00346 AC: 12 AN: 3466

East Asian (EAS) AF: 0.0669 AC: 345 AN: 5158

South Asian (SAS) AF: 0.0216 AC: 104 AN: 4812

European-Finnish (FIN) AF: 0.00361 AC: 38 AN: 10524

Middle Eastern (MID) AF: 0.00345 AC: 1 AN: 290

European-Non Finnish (NFE) AF: 0.00689 AC: 468 AN: 67970

Other (OTH) AF: 0.00758 AC: 16 AN: 2112

Alfa AF: 0.00736 Hom.: 2

Bravo AF: 0.0110

Asia WGS AF: 0.0540 AC: 187 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.32
CADD	Benign	15
DANN	Benign	0.55
PhyloP100		0.15

Splicing

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

Other links and lift over

dbSNP: rs10503053; hg19: chr18-58911181;