rs1941962

Variant names:

• chr18-51219099-C-G
• rs1941962

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 0.357 in 151,962 control chromosomes in the GnomAD database, including 10,741 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 0.36 (10741 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.756
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.445 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: 0.357 AC: 54276 AN: 151842 Hom.: 10745 Cov.: 32

Gnomad AFR AF: 0.203

Gnomad AMI AF: 0.355

Gnomad AMR AF: 0.345

Gnomad ASJ AF: 0.451

Gnomad EAS AF: 0.229

Gnomad SAS AF: 0.348

Gnomad FIN AF: 0.424

Gnomad MID AF: 0.340

Gnomad NFE AF: 0.449

Gnomad OTH AF: 0.372

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

GnomAD4 genome AF: 0.357 AC: 54282 AN: 151962 Hom.: 10741 Cov.: 32 AF XY: 0.354 AC XY: 26300 AN XY: 74284

African (AFR) AF: 0.203 AC: 8421 AN: 41466

American (AMR) AF: 0.345 AC: 5266 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.451 AC: 1566 AN: 3470

East Asian (EAS) AF: 0.230 AC: 1185 AN: 5160

South Asian (SAS) AF: 0.347 AC: 1669 AN: 4816

European-Finnish (FIN) AF: 0.424 AC: 4470 AN: 10538

Middle Eastern (MID) AF: 0.339 AC: 99 AN: 292

European-Non Finnish (NFE) AF: 0.449 AC: 30503 AN: 67932

Other (OTH) AF: 0.369 AC: 779 AN: 2112

Alfa AF: 0.408 Hom.: 1658

Bravo AF: 0.341

Asia WGS AF: 0.264 AC: 916 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.8
DANN	Benign	0.57
PhyloP100		-0.76

Splicing

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

Other links and lift over

dbSNP: rs1941962; hg19: chr18-48745469;