rs1319462

Variant names:

• chr14-61752507-G-A
• rs1319462
• ENST00000555937.1:n.149-14369G>A

Your query was ambiguous. Multiple possible variants found:

• chr14-61752507-G-A
• chr14-61752507-G-T

Variant summary

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

The ENST00000555937.1(ENSG00000258964):​n.149-14369G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.797 in 152,220 control chromosomes in the GnomAD database, including 48,812 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 0.80 (48812 hom., cov: 33)
• Consequence: ENSG00000258964 ENST00000555937.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.67

Genes affected

ENSG00000258964 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.838 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
ENSG00000258964	ENST00000555937.1	n.149-14369G>A		intron_variant	Intron 1 of 4	4

Frequencies

GnomAD3 genomes AF: 0.797 AC: 121180 AN: 152102 Hom.: 48756 Cov.: 33

Gnomad AFR AF: 0.691

Gnomad AMI AF: 0.839

Gnomad AMR AF: 0.831

Gnomad ASJ AF: 0.713

Gnomad EAS AF: 0.763

Gnomad SAS AF: 0.693

Gnomad FIN AF: 0.947

Gnomad MID AF: 0.709

Gnomad NFE AF: 0.844

Gnomad OTH AF: 0.786

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

GnomAD4 genome AF: 0.797 AC: 121301 AN: 152220 Hom.: 48812 Cov.: 33 AF XY: 0.799 AC XY: 59477 AN XY: 74424

Gnomad4 AFR AF: 0.691

Gnomad4 AMR AF: 0.831

Gnomad4 ASJ AF: 0.713

Gnomad4 EAS AF: 0.764

Gnomad4 SAS AF: 0.693

Gnomad4 FIN AF: 0.947

Gnomad4 NFE AF: 0.844

Gnomad4 OTH AF: 0.788

Alfa AF: 0.822 Hom.: 60968

Bravo AF: 0.787

Asia WGS AF: 0.737 AC: 2565 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.015
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1319462; hg19: chr14-62219225;