rs708495

Variant names:

• chr14-52302622-T-A
• rs708495
• ENST00000726797.1:n.299+10214A>T

Variant summary

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

The ENST00000726797.1(ENSG00000289424):​n.299+10214A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.568 in 152,040 control chromosomes in the GnomAD database, including 25,028 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 0.57 (25028 hom., cov: 32)
• Consequence: ENSG00000289424 ENST00000726797.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.335
• Publications: 2 publications found

Genes affected

ENSG00000289424 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.62 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
ENSG00000289424	ENST00000726797.1	n.299+10214A>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.568 AC: 86344 AN: 151922 Hom.: 25013 Cov.: 32

Gnomad AFR AF: 0.527

Gnomad AMI AF: 0.620

Gnomad AMR AF: 0.519

Gnomad ASJ AF: 0.595

Gnomad EAS AF: 0.424

Gnomad SAS AF: 0.364

Gnomad FIN AF: 0.592

Gnomad MID AF: 0.564

Gnomad NFE AF: 0.625

Gnomad OTH AF: 0.565

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

GnomAD4 genome AF: 0.568 AC: 86398 AN: 152040 Hom.: 25028 Cov.: 32 AF XY: 0.562 AC XY: 41733 AN XY: 74316

African (AFR) AF: 0.527 AC: 21840 AN: 41432

American (AMR) AF: 0.519 AC: 7933 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.595 AC: 2067 AN: 3472

East Asian (EAS) AF: 0.424 AC: 2194 AN: 5176

South Asian (SAS) AF: 0.363 AC: 1748 AN: 4818

European-Finnish (FIN) AF: 0.592 AC: 6241 AN: 10546

Middle Eastern (MID) AF: 0.562 AC: 164 AN: 292

European-Non Finnish (NFE) AF: 0.625 AC: 42462 AN: 67990

Other (OTH) AF: 0.561 AC: 1185 AN: 2112

Alfa AF: 0.593 Hom.: 3372

Bravo AF: 0.566

Asia WGS AF: 0.427 AC: 1485 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.5
DANN	Benign	0.88
PhyloP100		0.34

Splicing

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

Other links and lift over

dbSNP: rs708495; hg19: chr14-52769340;