chr14-64386187-C-T

Variant names:

• chr14-64386187-C-T
• rs1956545
• ENST00000689962.2:n.1793G>A

Variant summary

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

The ENST00000689962.2(ENSG00000293482):​n.1793G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.915 in 152,242 control chromosomes in the GnomAD database, including 64,282 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 0.92 (64282 hom., cov: 32)
• Consequence: ENSG00000293482 ENST00000689962.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.50
• Publications: 15 publications found

Genes affected

ENSG00000293482 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.947 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
ENSG00000293482	ENST00000689962.2	n.1793G>A		non_coding_transcript_exon_variant	Exon 1 of 1
ENSG00000293482	ENST00000641479.1	n.570+1230G>A		intron_variant	Intron 1 of 6
ENSG00000293482	ENST00000641725.1	n.465+402G>A		intron_variant	Intron 1 of 5

Frequencies

GnomAD3 genomes AF: 0.915 AC: 139239 AN: 152124 Hom.: 64234 Cov.: 32

Gnomad AFR AF: 0.955

Gnomad AMI AF: 0.943

Gnomad AMR AF: 0.934

Gnomad ASJ AF: 0.946

Gnomad EAS AF: 0.523

Gnomad SAS AF: 0.886

Gnomad FIN AF: 0.886

Gnomad MID AF: 0.962

Gnomad NFE AF: 0.921

Gnomad OTH AF: 0.930

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

GnomAD4 genome AF: 0.915 AC: 139350 AN: 152242 Hom.: 64282 Cov.: 32 AF XY: 0.912 AC XY: 67895 AN XY: 74430

African (AFR) AF: 0.955 AC: 39677 AN: 41556

American (AMR) AF: 0.934 AC: 14265 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.946 AC: 3283 AN: 3472

East Asian (EAS) AF: 0.524 AC: 2710 AN: 5174

South Asian (SAS) AF: 0.886 AC: 4270 AN: 4820

European-Finnish (FIN) AF: 0.886 AC: 9393 AN: 10598

Middle Eastern (MID) AF: 0.966 AC: 284 AN: 294

European-Non Finnish (NFE) AF: 0.921 AC: 62649 AN: 68034

Other (OTH) AF: 0.928 AC: 1961 AN: 2114

Alfa AF: 0.918 Hom.: 70270

Bravo AF: 0.920

Asia WGS AF: 0.735 AC: 2558 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.28
DANN	Benign	0.78
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs1956545; hg19: chr14-64852905;