rs1958305

Variant names:

• chr14-23803915-G-A
• rs1958305

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 0.158 in 152,110 control chromosomes in the GnomAD database, including 1,940 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 0.16 (1940 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.227

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.162 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: 0.158 AC: 23996 AN: 151990 Hom.: 1937 Cov.: 32

Gnomad AFR AF: 0.161

Gnomad AMI AF: 0.300

Gnomad AMR AF: 0.128

Gnomad ASJ AF: 0.161

Gnomad EAS AF: 0.0837

Gnomad SAS AF: 0.133

Gnomad FIN AF: 0.186

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.165

Gnomad OTH AF: 0.139

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

GnomAD4 genome AF: 0.158 AC: 24023 AN: 152110 Hom.: 1940 Cov.: 32 AF XY: 0.160 AC XY: 11868 AN XY: 74350

Gnomad4 AFR AF: 0.161

Gnomad4 AMR AF: 0.128

Gnomad4 ASJ AF: 0.161

Gnomad4 EAS AF: 0.0834

Gnomad4 SAS AF: 0.134

Gnomad4 FIN AF: 0.186

Gnomad4 NFE AF: 0.165

Gnomad4 OTH AF: 0.137

Alfa AF: 0.159 Hom.: 312

Bravo AF: 0.153

Asia WGS AF: 0.111 AC: 386 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.1
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1958305; hg19: chr14-24273124;