ENST00000443504.1:n.105-12350G>A

Variant names:

• chr6-19302945-C-T
• rs1390459
• ENST00000443504.1:n.105-12350G>A

Variant summary

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

The ENST00000443504.1(ENSG00000231662):​n.105-12350G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.814 in 152,024 control chromosomes in the GnomAD database, including 51,437 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 0.81 (51437 hom., cov: 31)
• Consequence: ENSG00000231662 ENST00000443504.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.771
• Publications: 0 publications found

Genes affected

ENSG00000231662 (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 (NFE) allele frequency at 95% confidence interval = 0.899 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
ENSG00000231662	ENST00000443504.1	n.105-12350G>A		intron_variant	Intron 1 of 1	3

Frequencies

GnomAD3 genomes AF: 0.814 AC: 123604 AN: 151906 Hom.: 51409 Cov.: 31

Gnomad AFR AF: 0.637

Gnomad AMI AF: 0.804

Gnomad AMR AF: 0.796

Gnomad ASJ AF: 0.881

Gnomad EAS AF: 0.821

Gnomad SAS AF: 0.805

Gnomad FIN AF: 0.924

Gnomad MID AF: 0.804

Gnomad NFE AF: 0.905

Gnomad OTH AF: 0.817

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

GnomAD4 genome AF: 0.814 AC: 123682 AN: 152024 Hom.: 51437 Cov.: 31 AF XY: 0.814 AC XY: 60470 AN XY: 74322

African (AFR) AF: 0.636 AC: 26340 AN: 41396

American (AMR) AF: 0.796 AC: 12150 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.881 AC: 3059 AN: 3472

East Asian (EAS) AF: 0.822 AC: 4234 AN: 5152

South Asian (SAS) AF: 0.805 AC: 3875 AN: 4816

European-Finnish (FIN) AF: 0.924 AC: 9782 AN: 10592

Middle Eastern (MID) AF: 0.816 AC: 240 AN: 294

European-Non Finnish (NFE) AF: 0.905 AC: 61543 AN: 68014

Other (OTH) AF: 0.816 AC: 1726 AN: 2116

Alfa AF: 0.875 Hom.: 83302

Bravo AF: 0.796

Asia WGS AF: 0.807 AC: 2802 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.47
DANN	Benign	0.84
PhyloP100		-0.77

Splicing

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

Other links and lift over

dbSNP: rs1390459; hg19: chr6-19303176;