rs1956716

Variant names:

• chr14-94459311-C-A
• rs1956716
• ENST00000536735.1:n.172-5023C>A

Variant summary

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

The ENST00000536735.1(ENSG00000256357):​n.172-5023C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.372 in 152,048 control chromosomes in the GnomAD database, including 11,251 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 0.37 (11251 hom., cov: 31)
• Consequence: ENSG00000256357 ENST00000536735.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.305
• Publications: 4 publications found

Genes affected

ENSG00000256357 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.458 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
ENSG00000256357	ENST00000536735.1	n.172-5023C>A		intron_variant	Intron 2 of 2	4
ENSG00000256357	ENST00000811346.1	n.355-2471C>A		intron_variant	Intron 2 of 2
ENSG00000256357	ENST00000811347.1	n.336-2007C>A		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.372 AC: 56559 AN: 151930 Hom.: 11248 Cov.: 31

Gnomad AFR AF: 0.235

Gnomad AMI AF: 0.499

Gnomad AMR AF: 0.459

Gnomad ASJ AF: 0.442

Gnomad EAS AF: 0.444

Gnomad SAS AF: 0.474

Gnomad FIN AF: 0.367

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.418

Gnomad OTH AF: 0.404

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

GnomAD4 genome AF: 0.372 AC: 56594 AN: 152048 Hom.: 11251 Cov.: 31 AF XY: 0.373 AC XY: 27693 AN XY: 74322

African (AFR) AF: 0.235 AC: 9734 AN: 41492

American (AMR) AF: 0.458 AC: 7004 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.442 AC: 1533 AN: 3470

East Asian (EAS) AF: 0.444 AC: 2292 AN: 5158

South Asian (SAS) AF: 0.474 AC: 2281 AN: 4808

European-Finnish (FIN) AF: 0.367 AC: 3875 AN: 10572

Middle Eastern (MID) AF: 0.412 AC: 121 AN: 294

European-Non Finnish (NFE) AF: 0.418 AC: 28432 AN: 67950

Other (OTH) AF: 0.410 AC: 867 AN: 2114

Alfa AF: 0.371 Hom.: 1379

Bravo AF: 0.370

Asia WGS AF: 0.476 AC: 1658 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.5
DANN	Benign	0.33
PhyloP100		0.30

Splicing

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

Other links and lift over

dbSNP: rs1956716; hg19: chr14-94925648;