chr14-25270440-G-A

Variant names:

• chr14-25270440-G-A
• rs961482
• ENST00000837960.1:n.380-8583G>A

Variant summary

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

The ENST00000837960.1(ENSG00000309034):​n.380-8583G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.66 in 151,992 control chromosomes in the GnomAD database, including 33,302 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 0.66 (33302 hom., cov: 31)
• Consequence: ENSG00000309034 ENST00000837960.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.160
• Publications: 1 publications found

Genes affected

ENSG00000309034 (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 (EAS) allele frequency at 95% confidence interval = 0.754 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000837960.1. 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
	ENSG00000309034	ENST00000837960.1		n.380-8583G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.660 AC: 100194 AN: 151874 Hom.: 33256 Cov.: 31

Gnomad AFR AF: 0.721

Gnomad AMI AF: 0.525

Gnomad AMR AF: 0.600

Gnomad ASJ AF: 0.572

Gnomad EAS AF: 0.774

Gnomad SAS AF: 0.711

Gnomad FIN AF: 0.671

Gnomad MID AF: 0.672

Gnomad NFE AF: 0.629

Gnomad OTH AF: 0.631

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

GnomAD4 genome AF: 0.660 AC: 100298 AN: 151992 Hom.: 33302 Cov.: 31 AF XY: 0.662 AC XY: 49184 AN XY: 74280

African (AFR) AF: 0.721 AC: 29908 AN: 41456

American (AMR) AF: 0.601 AC: 9183 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.572 AC: 1983 AN: 3466

East Asian (EAS) AF: 0.774 AC: 3991 AN: 5156

South Asian (SAS) AF: 0.712 AC: 3425 AN: 4808

European-Finnish (FIN) AF: 0.671 AC: 7082 AN: 10560

Middle Eastern (MID) AF: 0.675 AC: 197 AN: 292

European-Non Finnish (NFE) AF: 0.629 AC: 42712 AN: 67944

Other (OTH) AF: 0.635 AC: 1339 AN: 2110

Alfa AF: 0.638 Hom.: 15656

Bravo AF: 0.653

Asia WGS AF: 0.781 AC: 2716 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.54
DANN	Benign	0.64
PhyloP100		-0.16

Splicing

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

Other links and lift over

dbSNP: rs961482; hg19: chr14-25739646;