chr14-65291924-G-A

Variant names:

• chr14-65291924-G-A
• rs7159888
• ENST00000553754.1:n.301-22412C>T

Variant summary

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

The ENST00000553754.1(ENSG00000258760):​n.301-22412C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.522 in 152,054 control chromosomes in the GnomAD database, including 21,847 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 0.52 (21847 hom., cov: 32)
• Consequence: ENSG00000258760 ENST00000553754.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.230
• Publications: 18 publications found

Genes affected

ENSG00000258760 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.741 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000553754.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000258760	ENST00000553754.1	TSL:4	n.301-22412C>T		intron	N/A
	ENSG00000258760	ENST00000555736.1	TSL:5	n.152+10605C>T		intron	N/A
	ENSG00000302621	ENST00000788187.1		n.131+3817G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.521 AC: 79233 AN: 151936 Hom.: 21803 Cov.: 32

Gnomad AFR AF: 0.668

Gnomad AMI AF: 0.273

Gnomad AMR AF: 0.522

Gnomad ASJ AF: 0.519

Gnomad EAS AF: 0.760

Gnomad SAS AF: 0.624

Gnomad FIN AF: 0.539

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.408

Gnomad OTH AF: 0.522

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

GnomAD4 genome AF: 0.522 AC: 79331 AN: 152054 Hom.: 21847 Cov.: 32 AF XY: 0.531 AC XY: 39459 AN XY: 74342

African (AFR) AF: 0.668 AC: 27705 AN: 41476

American (AMR) AF: 0.522 AC: 7984 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.519 AC: 1802 AN: 3470

East Asian (EAS) AF: 0.760 AC: 3921 AN: 5156

South Asian (SAS) AF: 0.622 AC: 2995 AN: 4816

European-Finnish (FIN) AF: 0.539 AC: 5695 AN: 10572

Middle Eastern (MID) AF: 0.524 AC: 154 AN: 294

European-Non Finnish (NFE) AF: 0.408 AC: 27713 AN: 67966

Other (OTH) AF: 0.527 AC: 1113 AN: 2110

Alfa AF: 0.449 Hom.: 67419

Bravo AF: 0.527

Asia WGS AF: 0.721 AC: 2506 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.70
DANN	Benign	0.63
PhyloP100		-0.23

Splicing

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

Other links and lift over

dbSNP: rs7159888; hg19: chr14-65758642;