rs17049105

Variant names:

• chr2-57745476-A-G
• rs17049105
• ENST00000811253.1:n.148+36817T>C

Variant summary

Our verdict is Benign. The variant received -9 ACMG points: 0P and 9B. BP4 BA1

The ENST00000811253.1(ENSG00000285755):​n.148+36817T>C variant causes a intron change. The variant allele was found at a frequency of 0.0995 in 152,176 control chromosomes in the GnomAD database, including 792 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 0.10 (792 hom., cov: 32)
• Consequence: ENSG00000285755 ENST00000811253.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 6.02
• Publications: 3 publications found

Genes affected

ENSG00000285755 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -9 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.18).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.164 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
ENSG00000285755	ENST00000811253.1	n.148+36817T>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.0995 AC: 15134 AN: 152058 Hom.: 792 Cov.: 32

Gnomad AFR AF: 0.101

Gnomad AMI AF: 0.158

Gnomad AMR AF: 0.111

Gnomad ASJ AF: 0.0683

Gnomad EAS AF: 0.174

Gnomad SAS AF: 0.0882

Gnomad FIN AF: 0.160

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0829

Gnomad OTH AF: 0.0866

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

GnomAD4 genome AF: 0.0995 AC: 15147 AN: 152176 Hom.: 792 Cov.: 32 AF XY: 0.104 AC XY: 7746 AN XY: 74402

African (AFR) AF: 0.101 AC: 4203 AN: 41544

American (AMR) AF: 0.112 AC: 1704 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.0683 AC: 237 AN: 3472

East Asian (EAS) AF: 0.174 AC: 901 AN: 5188

South Asian (SAS) AF: 0.0877 AC: 423 AN: 4824

European-Finnish (FIN) AF: 0.160 AC: 1696 AN: 10592

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.0829 AC: 5638 AN: 67972

Other (OTH) AF: 0.0852 AC: 180 AN: 2112

Alfa AF: 0.0933 Hom.: 97

Bravo AF: 0.0967

Asia WGS AF: 0.114 AC: 395 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.18
CADD	Benign	23
DANN	Benign	0.86
PhyloP100		6.0

Splicing

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

Other links and lift over

dbSNP: rs17049105; hg19: chr2-57972611;