rs783149

Variant names:

• chr6-160667886-C-A
• rs783149
• ENST00000452651.1:n.115-1513G>T

Variant summary

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

The ENST00000452651.1(ENSG00000243831):​n.115-1513G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.253 in 152,076 control chromosomes in the GnomAD database, including 5,704 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 0.25 (5704 hom., cov: 32)
• Consequence: ENSG00000243831 ENST00000452651.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.332
• Publications: 18 publications found

Genes affected

ENSG00000243831 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.44 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
ENSG00000243831	ENST00000452651.1	n.115-1513G>T		intron_variant	Intron 1 of 1	6
ENSG00000303834	ENST00000797429.1	n.478+158G>T		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.252 AC: 38361 AN: 151958 Hom.: 5688 Cov.: 32

Gnomad AFR AF: 0.357

Gnomad AMI AF: 0.0658

Gnomad AMR AF: 0.358

Gnomad ASJ AF: 0.137

Gnomad EAS AF: 0.455

Gnomad SAS AF: 0.306

Gnomad FIN AF: 0.177

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.167

Gnomad OTH AF: 0.235

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

GnomAD4 genome AF: 0.253 AC: 38415 AN: 152076 Hom.: 5704 Cov.: 32 AF XY: 0.256 AC XY: 19037 AN XY: 74358

African (AFR) AF: 0.357 AC: 14799 AN: 41462

American (AMR) AF: 0.358 AC: 5472 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.137 AC: 474 AN: 3468

East Asian (EAS) AF: 0.456 AC: 2350 AN: 5158

South Asian (SAS) AF: 0.306 AC: 1471 AN: 4812

European-Finnish (FIN) AF: 0.177 AC: 1880 AN: 10608

Middle Eastern (MID) AF: 0.221 AC: 65 AN: 294

European-Non Finnish (NFE) AF: 0.167 AC: 11353 AN: 67986

Other (OTH) AF: 0.233 AC: 491 AN: 2110

Alfa AF: 0.195 Hom.: 10833

Bravo AF: 0.272

Asia WGS AF: 0.378 AC: 1313 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.6
DANN	Benign	0.36
PhyloP100		-0.33

Splicing

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

Other links and lift over

dbSNP: rs783149; hg19: chr6-161088918;