14-34665980-A-G

Variant names:

• chr14-34665980-A-G
• rs7141276
• ENST00000812536.1:n.141-14483T>C

Variant summary

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

The ENST00000812536.1(ENSG00000305710):​n.141-14483T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.483 in 151,984 control chromosomes in the GnomAD database, including 19,019 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 0.48 (19019 hom., cov: 32)
• Consequence: ENSG00000305710 ENST00000812536.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.175
• Publications: 11 publications found

Genes affected

ENSG00000305710 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.662 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000812536.1. 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
	ENSG00000305710	ENST00000812536.1		n.141-14483T>C		intron	N/A
	ENSG00000305710	ENST00000812537.1		n.431-14483T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.483 AC: 73322 AN: 151866 Hom.: 18991 Cov.: 32

Gnomad AFR AF: 0.669

Gnomad AMI AF: 0.297

Gnomad AMR AF: 0.513

Gnomad ASJ AF: 0.374

Gnomad EAS AF: 0.571

Gnomad SAS AF: 0.398

Gnomad FIN AF: 0.396

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.385

Gnomad OTH AF: 0.450

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

GnomAD4 genome AF: 0.483 AC: 73404 AN: 151984 Hom.: 19019 Cov.: 32 AF XY: 0.483 AC XY: 35863 AN XY: 74288

African (AFR) AF: 0.669 AC: 27702 AN: 41426

American (AMR) AF: 0.514 AC: 7844 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.374 AC: 1295 AN: 3466

East Asian (EAS) AF: 0.570 AC: 2950 AN: 5172

South Asian (SAS) AF: 0.400 AC: 1928 AN: 4822

European-Finnish (FIN) AF: 0.396 AC: 4186 AN: 10572

Middle Eastern (MID) AF: 0.384 AC: 113 AN: 294

European-Non Finnish (NFE) AF: 0.385 AC: 26171 AN: 67944

Other (OTH) AF: 0.449 AC: 945 AN: 2106

Alfa AF: 0.427 Hom.: 13156

Bravo AF: 0.505

Asia WGS AF: 0.478 AC: 1665 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.6
DANN	Benign	0.82
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs7141276; hg19: chr14-35135186;