14-35424419-G-T

Variant names:

• chr14-35424419-G-T
• rs4982271
• ENST00000848537.1:n.241+21032G>T

Variant summary

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

The ENST00000848537.1(ENSG00000310246):​n.241+21032G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.573 in 151,958 control chromosomes in the GnomAD database, including 25,802 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 0.57 (25802 hom., cov: 31)
• Consequence: ENSG00000310246 ENST00000848537.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.221
• Publications: 6 publications found

Genes affected

ENSG00000310246 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.695 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000848537.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000310246	ENST00000848537.1		n.241+21032G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.573 AC: 86940 AN: 151840 Hom.: 25759 Cov.: 31

Gnomad AFR AF: 0.701

Gnomad AMI AF: 0.530

Gnomad AMR AF: 0.609

Gnomad ASJ AF: 0.432

Gnomad EAS AF: 0.713

Gnomad SAS AF: 0.550

Gnomad FIN AF: 0.593

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.483

Gnomad OTH AF: 0.538

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

GnomAD4 genome AF: 0.573 AC: 87045 AN: 151958 Hom.: 25802 Cov.: 31 AF XY: 0.580 AC XY: 43075 AN XY: 74278

African (AFR) AF: 0.702 AC: 29070 AN: 41438

American (AMR) AF: 0.610 AC: 9293 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.432 AC: 1496 AN: 3466

East Asian (EAS) AF: 0.713 AC: 3688 AN: 5174

South Asian (SAS) AF: 0.548 AC: 2642 AN: 4822

European-Finnish (FIN) AF: 0.593 AC: 6256 AN: 10556

Middle Eastern (MID) AF: 0.425 AC: 124 AN: 292

European-Non Finnish (NFE) AF: 0.483 AC: 32849 AN: 67944

Other (OTH) AF: 0.542 AC: 1145 AN: 2114

Alfa AF: 0.529 Hom.: 5738

Bravo AF: 0.579

Asia WGS AF: 0.679 AC: 2357 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.3
DANN	Benign	0.42
PhyloP100		0.22

Splicing

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

Other links and lift over

dbSNP: rs4982271; hg19: chr14-35893625;