chr6-14719265-G-A

Variant names:

• chr6-14719265-G-A
• rs17119
• ENST00000629853.3:n.314-56972C>T

Variant summary

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

The ENST00000629853.3(ENSG00000234261):​n.314-56972C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.743 in 152,198 control chromosomes in the GnomAD database, including 42,770 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 0.74 (42770 hom., cov: 33)
• Consequence: ENSG00000234261 ENST00000629853.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0880
• Publications: 49 publications found

Genes affected

ENSG00000234261 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.901 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
ENSG00000234261	ENST00000629853.3	n.314-56972C>T		intron_variant	Intron 3 of 3	5
ENSG00000234261	ENST00000689305.1	n.230+21735C>T		intron_variant	Intron 2 of 2
ENSG00000234261	ENST00000729738.1	n.110+70725C>T		intron_variant	Intron 1 of 7

Frequencies

GnomAD3 genomes AF: 0.743 AC: 112990 AN: 152078 Hom.: 42751 Cov.: 33

Gnomad AFR AF: 0.595

Gnomad AMI AF: 0.819

Gnomad AMR AF: 0.705

Gnomad ASJ AF: 0.684

Gnomad EAS AF: 0.923

Gnomad SAS AF: 0.775

Gnomad FIN AF: 0.901

Gnomad MID AF: 0.634

Gnomad NFE AF: 0.804

Gnomad OTH AF: 0.709

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

GnomAD4 genome AF: 0.743 AC: 113052 AN: 152198 Hom.: 42770 Cov.: 33 AF XY: 0.748 AC XY: 55657 AN XY: 74420

African (AFR) AF: 0.595 AC: 24667 AN: 41476

American (AMR) AF: 0.705 AC: 10778 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.684 AC: 2374 AN: 3472

East Asian (EAS) AF: 0.923 AC: 4788 AN: 5186

South Asian (SAS) AF: 0.775 AC: 3737 AN: 4822

European-Finnish (FIN) AF: 0.901 AC: 9566 AN: 10618

Middle Eastern (MID) AF: 0.643 AC: 189 AN: 294

European-Non Finnish (NFE) AF: 0.804 AC: 54700 AN: 68016

Other (OTH) AF: 0.713 AC: 1506 AN: 2112

Alfa AF: 0.777 Hom.: 179936

Bravo AF: 0.721

Asia WGS AF: 0.812 AC: 2825 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.4
DANN	Benign	0.53
PhyloP100		0.088

Splicing

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

Other links and lift over

dbSNP: rs17119; hg19: chr6-14719496;