14-61752507-G-A

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 12 publications found

Genes affected

ENSG00000258964 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000555937.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000258964	ENST00000555937.1	TSL:4	n.149-14369G>A		intron	N/A

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

African (AFR) AF: 0.691 AC: 28676 AN: 41470

American (AMR) AF: 0.831 AC: 12716 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.713 AC: 2473 AN: 3470

East Asian (EAS) AF: 0.764 AC: 3963 AN: 5188

South Asian (SAS) AF: 0.693 AC: 3349 AN: 4832

European-Finnish (FIN) AF: 0.947 AC: 10044 AN: 10606

Middle Eastern (MID) AF: 0.718 AC: 211 AN: 294

European-Non Finnish (NFE) AF: 0.844 AC: 57437 AN: 68034

Other (OTH) AF: 0.788 AC: 1667 AN: 2116

Alfa AF: 0.819 Hom.: 75444

Bravo AF: 0.787

Asia WGS AF: 0.737 AC: 2565 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.015
DANN	Benign	0.81
PhyloP100		-2.7

Splicing

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

Other links and lift over

dbSNP: rs1319462; hg19: chr14-62219225;