chr14-76698212-G-A

Variant names:

• chr14-76698212-G-A
• rs17104804
• ENST00000554926.1:n.194+28307C>T

Variant summary

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

The ENST00000554926.1(ENSG00000259124):​n.194+28307C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0729 in 152,174 control chromosomes in the GnomAD database, including 599 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 0.073 (599 hom., cov: 32)
• Consequence: ENSG00000259124 ENST00000554926.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.98
• Publications: 1 publications found

Genes affected

ENSG00000259124 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.278 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
ENSG00000259124	ENST00000554926.1	n.194+28307C>T		intron_variant	Intron 1 of 3	3
ENSG00000306597	ENST00000819589.1	n.432+7685C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0729 AC: 11086 AN: 152056 Hom.: 598 Cov.: 32

Gnomad AFR AF: 0.0393

Gnomad AMI AF: 0.0844

Gnomad AMR AF: 0.113

Gnomad ASJ AF: 0.0505

Gnomad EAS AF: 0.292

Gnomad SAS AF: 0.119

Gnomad FIN AF: 0.0691

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0661

Gnomad OTH AF: 0.0762

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

GnomAD4 genome AF: 0.0729 AC: 11098 AN: 152174 Hom.: 599 Cov.: 32 AF XY: 0.0768 AC XY: 5710 AN XY: 74390

African (AFR) AF: 0.0393 AC: 1633 AN: 41516

American (AMR) AF: 0.113 AC: 1734 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0505 AC: 175 AN: 3466

East Asian (EAS) AF: 0.290 AC: 1504 AN: 5178

South Asian (SAS) AF: 0.119 AC: 574 AN: 4822

European-Finnish (FIN) AF: 0.0691 AC: 731 AN: 10586

Middle Eastern (MID) AF: 0.0442 AC: 13 AN: 294

European-Non Finnish (NFE) AF: 0.0661 AC: 4492 AN: 67996

Other (OTH) AF: 0.0783 AC: 165 AN: 2108

Alfa AF: 0.0672 Hom.: 401

Bravo AF: 0.0756

Asia WGS AF: 0.181 AC: 630 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.057
DANN	Benign	0.67
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs17104804; hg19: chr14-77164555;