rs1390459

chr6-19302945-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000443504.1(ENSG00000231662):n.105-12350G>A variant causes a intron, non coding transcript 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: ENST00000443504.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.771

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000443504.1	n.105-12350G>A		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.636

Gnomad4 AMR AF: 0.796

Gnomad4 ASJ AF: 0.881

Gnomad4 EAS AF: 0.822

Gnomad4 SAS AF: 0.805

Gnomad4 FIN AF: 0.924

Gnomad4 NFE AF: 0.905

Gnomad4 OTH AF: 0.816

Alfa AF: 0.885 Hom.: 68461

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1390459; hg19: chr6-19303176;