rs1956923

Variant names:

• chr14-24508761-G-A
• rs1956923
• ENST00000555109.2:n.*61G>A

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000555109.2(ENSG00000258744):​n.*61G>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 ENST00000555109.2 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.643
• Publications: 4 publications found

Genes affected

ENSG00000258744 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000555109.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000258744	ENST00000555109.2	TSL:5	n.*61G>A		downstream_gene	N/A
	ENSG00000258744	ENST00000816252.1		n.*61G>A		downstream_gene	N/A

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

African (AFR) AF: 0.00 AC: 0 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 1.00 AC: 2 AN: 2

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.262 AC: 11 AN: 42

Other (OTH) AF: 1.00 AC: 2 AN: 2

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

African (AFR) AF: 0.270 AC: 11206 AN: 41428

American (AMR) AF: 0.471 AC: 7186 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.326 AC: 1131 AN: 3468

East Asian (EAS) AF: 0.415 AC: 2148 AN: 5178

South Asian (SAS) AF: 0.323 AC: 1554 AN: 4814

European-Finnish (FIN) AF: 0.346 AC: 3640 AN: 10512

Middle Eastern (MID) AF: 0.350 AC: 103 AN: 294

European-Non Finnish (NFE) AF: 0.262 AC: 17807 AN: 67942

Other (OTH) AF: 0.318 AC: 670 AN: 2106

Alfa AF: 0.270 Hom.: 1374

Bravo AF: 0.313

Asia WGS AF: 0.380 AC: 1323 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	6.9
DANN	Benign	0.80
PhyloP100		-0.64
PromoterAI		-0.050	Neutral

Splicing

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

Other links and lift over

dbSNP: rs1956923; hg19: chr14-24977967;