rs1946234

Positions:

• chr5-151019649-A-C

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 0.151 in 152,122 control chromosomes in the GnomAD database, including 1,831 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 0.15 (1831 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.467

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.206 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.151 AC: 23001 AN: 152002 Hom.: 1827 Cov.: 32

Gnomad AFR AF: 0.210

Gnomad AMI AF: 0.242

Gnomad AMR AF: 0.0955

Gnomad ASJ AF: 0.129

Gnomad EAS AF: 0.171

Gnomad SAS AF: 0.150

Gnomad FIN AF: 0.110

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.133

Gnomad OTH AF: 0.140

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

GnomAD4 genome AF: 0.151 AC: 23026 AN: 152122 Hom.: 1831 Cov.: 32 AF XY: 0.149 AC XY: 11052 AN XY: 74390

Gnomad4 AFR AF: 0.210

Gnomad4 AMR AF: 0.0953

Gnomad4 ASJ AF: 0.129

Gnomad4 EAS AF: 0.171

Gnomad4 SAS AF: 0.151

Gnomad4 FIN AF: 0.110

Gnomad4 NFE AF: 0.133

Gnomad4 OTH AF: 0.138

Alfa AF: 0.133 Hom.: 1887

Bravo AF: 0.151

Asia WGS AF: 0.152 AC: 530 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.23
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1946234; hg19: chr5-150399210;