chr14-100693079-T-G

Variant names:

• chr14-100693079-T-G
• rs7149242
• ENST00000761489.1:n.254+4610A>C

Variant summary

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

The ENST00000761489.1(ENSG00000258717):​n.254+4610A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.619 in 152,124 control chromosomes in the GnomAD database, including 30,540 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 0.62 (30540 hom., cov: 33)
• Consequence: ENSG00000258717 ENST00000761489.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.527
• Publications: 25 publications found

Genes affected

ENSG00000258717 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.718 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000761489.1. 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
	ENSG00000258717	ENST00000761489.1		n.254+4610A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.619 AC: 94114 AN: 152006 Hom.: 30513 Cov.: 33

Gnomad AFR AF: 0.419

Gnomad AMI AF: 0.793

Gnomad AMR AF: 0.694

Gnomad ASJ AF: 0.675

Gnomad EAS AF: 0.599

Gnomad SAS AF: 0.507

Gnomad FIN AF: 0.644

Gnomad MID AF: 0.725

Gnomad NFE AF: 0.724

Gnomad OTH AF: 0.643

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

GnomAD4 genome AF: 0.619 AC: 94177 AN: 152124 Hom.: 30540 Cov.: 33 AF XY: 0.615 AC XY: 45752 AN XY: 74370

African (AFR) AF: 0.419 AC: 17377 AN: 41516

American (AMR) AF: 0.695 AC: 10628 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.675 AC: 2343 AN: 3472

East Asian (EAS) AF: 0.599 AC: 3081 AN: 5144

South Asian (SAS) AF: 0.509 AC: 2451 AN: 4818

European-Finnish (FIN) AF: 0.644 AC: 6825 AN: 10604

Middle Eastern (MID) AF: 0.724 AC: 213 AN: 294

European-Non Finnish (NFE) AF: 0.724 AC: 49175 AN: 67958

Other (OTH) AF: 0.644 AC: 1361 AN: 2112

Alfa AF: 0.675 Hom.: 59241

Bravo AF: 0.617

Asia WGS AF: 0.543 AC: 1889 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.80
DANN	Benign	0.26
PhyloP100		-0.53

Splicing

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

Other links and lift over

dbSNP: rs7149242; hg19: chr14-101159416; COSMIC: COSV68250653;