rs1941962

chr18-51219099-C-G

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;