rs708495

Variant names:

• chr14-52302622-T-A
• rs708495

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 0.568 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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.335

ACMG classification

Verdict is Benign. Variant got -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

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

Gnomad4 AFR AF: 0.527

Gnomad4 AMR AF: 0.519

Gnomad4 ASJ AF: 0.595

Gnomad4 EAS AF: 0.424

Gnomad4 SAS AF: 0.363

Gnomad4 FIN AF: 0.592

Gnomad4 NFE AF: 0.625

Gnomad4 OTH AF: 0.561

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs708495; hg19: chr14-52769340;