rs1956923

Variant names:

• chr14-24508761-G-A
• rs1956923
• ENST00000555109.1:n.*73G>A

Your query was ambiguous. Multiple possible variants found:

• chr14-24508761-G-A
• chr14-24508761-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000555109.1(ENSG00000258744):​n.*73G>A variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.301 in 151,970 control chromosomes in the GnomAD database, including 7,373 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 0.30 (7370 hom., cov: 32)
  • Exomes 𝑓: 0.31 (3 hom.)
• Consequence: ENSG00000258744 ENST00000555109.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.643

Genes affected

ENSG00000258744 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.462 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
ENSG00000258744	ENST00000555109.1	n.*73G>A		downstream_gene_variant		5

Frequencies

GnomAD3 genomes AF: 0.301 AC: 45716 AN: 151804 Hom.: 7357 Cov.: 32

Gnomad AFR AF: 0.271

Gnomad AMI AF: 0.351

Gnomad AMR AF: 0.470

Gnomad ASJ AF: 0.326

Gnomad EAS AF: 0.415

Gnomad SAS AF: 0.323

Gnomad FIN AF: 0.346

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.262

Gnomad OTH AF: 0.319

GnomAD4 exome AF: 0.313 AC: 15 AN: 48 Hom.: 3 AF XY: 0.269 AC XY: 7 AN XY: 26

Gnomad4 AFR exome AF: 0.00

Gnomad4 EAS exome AF: 1.00

Gnomad4 NFE exome AF: 0.262

Gnomad4 OTH exome AF: 1.00

GnomAD4 genome AF: 0.301 AC: 45764 AN: 151922 Hom.: 7370 Cov.: 32 AF XY: 0.311 AC XY: 23078 AN XY: 74240

Gnomad4 AFR AF: 0.270

Gnomad4 AMR AF: 0.471

Gnomad4 ASJ AF: 0.326

Gnomad4 EAS AF: 0.415

Gnomad4 SAS AF: 0.323

Gnomad4 FIN AF: 0.346

Gnomad4 NFE AF: 0.262

Gnomad4 OTH AF: 0.318

Alfa AF: 0.271 Hom.: 1344

Bravo AF: 0.313

Asia WGS AF: 0.380 AC: 1323 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	6.9
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1956923; hg19: chr14-24977967;