rs1545169

Variant names:

• chr5-111063678-T-G
• rs1545169
• ENST00000743602.1:n.29+2757A>C

Variant summary

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

The ENST00000743602.1(ENSG00000296915):​n.29+2757A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.112 in 152,186 control chromosomes in the GnomAD database, including 1,475 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 0.11 (1475 hom., cov: 31)
• Consequence: ENSG00000296915 ENST00000743602.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.45
• Publications: 3 publications found

Genes affected

ENSG00000296915 (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 (EAS) allele frequency at 95% confidence interval = 0.373 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
ENSG00000296915	ENST00000743602.1	n.29+2757A>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.112 AC: 16999 AN: 152068 Hom.: 1476 Cov.: 31

Gnomad AFR AF: 0.196

Gnomad AMI AF: 0.0516

Gnomad AMR AF: 0.0960

Gnomad ASJ AF: 0.0573

Gnomad EAS AF: 0.388

Gnomad SAS AF: 0.197

Gnomad FIN AF: 0.0653

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0490

Gnomad OTH AF: 0.0904

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

GnomAD4 genome AF: 0.112 AC: 17005 AN: 152186 Hom.: 1475 Cov.: 31 AF XY: 0.116 AC XY: 8643 AN XY: 74418

African (AFR) AF: 0.195 AC: 8110 AN: 41490

American (AMR) AF: 0.0961 AC: 1469 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0573 AC: 199 AN: 3472

East Asian (EAS) AF: 0.387 AC: 2003 AN: 5172

South Asian (SAS) AF: 0.197 AC: 952 AN: 4824

European-Finnish (FIN) AF: 0.0653 AC: 693 AN: 10618

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.0490 AC: 3329 AN: 68000

Other (OTH) AF: 0.0895 AC: 189 AN: 2112

Alfa AF: 0.0702 Hom.: 2909

Bravo AF: 0.116

Asia WGS AF: 0.247 AC: 857 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	0.26
DANN	Benign	0.70
PhyloP100		-2.5

Splicing

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

Other links and lift over

dbSNP: rs1545169; hg19: chr5-110399376;