chr13-103379989-G-T

Variant names:

• chr13-103379989-G-T
• rs1929081
• ENST00000648788.1:n.56-12238G>T

Variant summary

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

The ENST00000648788.1(ENSG00000285789):​n.56-12238G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.371 in 151,958 control chromosomes in the GnomAD database, including 12,540 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 0.37 (12540 hom., cov: 32)
• Consequence: ENSG00000285789 ENST00000648788.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.19
• Publications: 4 publications found

Genes affected

ENSG00000285789 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.627 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000648788.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000285789	ENST00000648788.1		n.56-12238G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.370 AC: 56226 AN: 151838 Hom.: 12501 Cov.: 32

Gnomad AFR AF: 0.633

Gnomad AMI AF: 0.118

Gnomad AMR AF: 0.274

Gnomad ASJ AF: 0.288

Gnomad EAS AF: 0.266

Gnomad SAS AF: 0.248

Gnomad FIN AF: 0.309

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.267

Gnomad OTH AF: 0.352

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

GnomAD4 genome AF: 0.371 AC: 56325 AN: 151958 Hom.: 12540 Cov.: 32 AF XY: 0.367 AC XY: 27253 AN XY: 74252

African (AFR) AF: 0.634 AC: 26245 AN: 41428

American (AMR) AF: 0.273 AC: 4168 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.288 AC: 998 AN: 3466

East Asian (EAS) AF: 0.266 AC: 1372 AN: 5158

South Asian (SAS) AF: 0.249 AC: 1199 AN: 4824

European-Finnish (FIN) AF: 0.309 AC: 3263 AN: 10560

Middle Eastern (MID) AF: 0.303 AC: 89 AN: 294

European-Non Finnish (NFE) AF: 0.267 AC: 18144 AN: 67952

Other (OTH) AF: 0.350 AC: 739 AN: 2110

Alfa AF: 0.297 Hom.: 4150

Bravo AF: 0.382

Asia WGS AF: 0.274 AC: 951 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.11
DANN	Benign	0.19
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs1929081; hg19: chr13-104032339;