14-40205737-G-T

Variant names:

• chr14-40205737-G-T
• rs735543
• ENST00000652126.1:n.521+78104G>T

Variant summary

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

The ENST00000652126.1(ENSG00000258526):​n.521+78104G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.555 in 152,072 control chromosomes in the GnomAD database, including 23,830 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 0.55 (23830 hom., cov: 32)
• Consequence: ENSG00000258526 ENST00000652126.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.144
• Publications: 3 publications found

Genes affected

ENSG00000258526 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.647 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000652126.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000258526	ENST00000652126.1		n.521+78104G>T		intron	N/A
	ENSG00000309779	ENST00000843857.1		n.179+10537C>A		intron	N/A
	ENSG00000309779	ENST00000843858.1		n.180-8050C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.555 AC: 84300 AN: 151954 Hom.: 23803 Cov.: 32

Gnomad AFR AF: 0.622

Gnomad AMI AF: 0.346

Gnomad AMR AF: 0.521

Gnomad ASJ AF: 0.480

Gnomad EAS AF: 0.666

Gnomad SAS AF: 0.599

Gnomad FIN AF: 0.393

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.543

Gnomad OTH AF: 0.539

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

GnomAD4 genome AF: 0.555 AC: 84375 AN: 152072 Hom.: 23830 Cov.: 32 AF XY: 0.548 AC XY: 40707 AN XY: 74340

African (AFR) AF: 0.622 AC: 25761 AN: 41440

American (AMR) AF: 0.521 AC: 7972 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.480 AC: 1665 AN: 3472

East Asian (EAS) AF: 0.666 AC: 3446 AN: 5174

South Asian (SAS) AF: 0.599 AC: 2891 AN: 4826

European-Finnish (FIN) AF: 0.393 AC: 4155 AN: 10584

Middle Eastern (MID) AF: 0.452 AC: 132 AN: 292

European-Non Finnish (NFE) AF: 0.543 AC: 36888 AN: 67968

Other (OTH) AF: 0.544 AC: 1149 AN: 2112

Alfa AF: 0.539 Hom.: 37068

Bravo AF: 0.568

Asia WGS AF: 0.626 AC: 2178 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.23
DANN	Benign	0.43
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs735543; hg19: chr14-40674941;