14-98947335-C-G

Variant names:

• chr14-98947335-C-G
• rs807339
• ENST00000724621.1:n.265-25434G>C

Variant summary

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

The ENST00000724621.1(ENSG00000294598):​n.265-25434G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.926 in 152,206 control chromosomes in the GnomAD database, including 65,616 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 0.93 (65616 hom., cov: 31)
• Consequence: ENSG00000294598 ENST00000724621.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.119
• Publications: 3 publications found

Genes affected

ENSG00000294598 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.975 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000294598	ENST00000724621.1	n.265-25434G>C		intron_variant	Intron 2 of 4
ENSG00000294598	ENST00000724623.1	n.213-1867G>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.926 AC: 140770 AN: 152088 Hom.: 65564 Cov.: 31

Gnomad AFR AF: 0.983

Gnomad AMI AF: 0.931

Gnomad AMR AF: 0.793

Gnomad ASJ AF: 0.947

Gnomad EAS AF: 0.728

Gnomad SAS AF: 0.883

Gnomad FIN AF: 0.939

Gnomad MID AF: 0.978

Gnomad NFE AF: 0.935

Gnomad OTH AF: 0.917

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

GnomAD4 genome AF: 0.926 AC: 140873 AN: 152206 Hom.: 65616 Cov.: 31 AF XY: 0.922 AC XY: 68619 AN XY: 74426

African (AFR) AF: 0.983 AC: 40823 AN: 41542

American (AMR) AF: 0.792 AC: 12102 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.947 AC: 3289 AN: 3472

East Asian (EAS) AF: 0.728 AC: 3750 AN: 5148

South Asian (SAS) AF: 0.883 AC: 4253 AN: 4816

European-Finnish (FIN) AF: 0.939 AC: 9964 AN: 10612

Middle Eastern (MID) AF: 0.976 AC: 287 AN: 294

European-Non Finnish (NFE) AF: 0.935 AC: 63623 AN: 68014

Other (OTH) AF: 0.917 AC: 1933 AN: 2108

Alfa AF: 0.924 Hom.: 3181

Bravo AF: 0.914

Asia WGS AF: 0.813 AC: 2829 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	2.6
DANN	Benign	0.41
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs807339; hg19: chr14-99413672;