rs1387929

Variant names:

• chr9-85173043-G-T
• rs1387929
• ENST00000649497.1:n.104+14G>T

Variant summary

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

The ENST00000649497.1(ENSG00000285556):​n.104+14G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.362 in 152,026 control chromosomes in the GnomAD database, including 10,546 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 0.36 (10546 hom., cov: 32)
• Consequence: ENSG00000285556 ENST00000649497.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.217

Genes affected

ENSG00000285556 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.426 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
ENSG00000285556	ENST00000649497.1	n.104+14G>T		intron_variant	Intron 2 of 6

Frequencies

GnomAD3 genomes AF: 0.362 AC: 54968 AN: 151908 Hom.: 10541 Cov.: 32

Gnomad AFR AF: 0.268

Gnomad AMI AF: 0.315

Gnomad AMR AF: 0.435

Gnomad ASJ AF: 0.427

Gnomad EAS AF: 0.146

Gnomad SAS AF: 0.219

Gnomad FIN AF: 0.408

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.419

Gnomad OTH AF: 0.374

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

GnomAD4 genome AF: 0.362 AC: 54998 AN: 152026 Hom.: 10546 Cov.: 32 AF XY: 0.358 AC XY: 26591 AN XY: 74304

Gnomad4 AFR AF: 0.268

Gnomad4 AMR AF: 0.435

Gnomad4 ASJ AF: 0.427

Gnomad4 EAS AF: 0.146

Gnomad4 SAS AF: 0.218

Gnomad4 FIN AF: 0.408

Gnomad4 NFE AF: 0.419

Gnomad4 OTH AF: 0.370

Alfa AF: 0.398 Hom.: 1995

Bravo AF: 0.360

Asia WGS AF: 0.182 AC: 631 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	5.6
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1387929; hg19: chr9-87787958;