rs1941962

Variant names:

• chr18-51219099-C-G
• rs1941962

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 0.357 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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.203

Gnomad4 AMR AF: 0.345

Gnomad4 ASJ AF: 0.451

Gnomad4 EAS AF: 0.230

Gnomad4 SAS AF: 0.347

Gnomad4 FIN AF: 0.424

Gnomad4 NFE AF: 0.449

Gnomad4 OTH AF: 0.369

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1941962; hg19: chr18-48745469;