rs955155

Variant names:

• chr19-39238839-G-A
• rs955155

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 0.197 in 152,188 control chromosomes in the GnomAD database, including 3,556 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 0.20 (3556 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.432

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.284 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: 0.197 AC: 29922 AN: 152070 Hom.: 3557 Cov.: 32

Gnomad AFR AF: 0.0811

Gnomad AMI AF: 0.253

Gnomad AMR AF: 0.292

Gnomad ASJ AF: 0.278

Gnomad EAS AF: 0.0624

Gnomad SAS AF: 0.193

Gnomad FIN AF: 0.232

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.245

Gnomad OTH AF: 0.218

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

GnomAD4 genome AF: 0.197 AC: 29929 AN: 152188 Hom.: 3556 Cov.: 32 AF XY: 0.196 AC XY: 14574 AN XY: 74380

Gnomad4 AFR AF: 0.0810

Gnomad4 AMR AF: 0.291

Gnomad4 ASJ AF: 0.278

Gnomad4 EAS AF: 0.0627

Gnomad4 SAS AF: 0.194

Gnomad4 FIN AF: 0.232

Gnomad4 NFE AF: 0.245

Gnomad4 OTH AF: 0.215

Alfa AF: 0.246 Hom.: 4542

Bravo AF: 0.198

Asia WGS AF: 0.128 AC: 448 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	11
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs955155; hg19: chr19-39729479;