rs2407103

Variant names:

• chr8-37094396-A-G
• rs2407103
• ENST00000744926.1:n.223-18284T>C

Your query was ambiguous. Multiple possible variants found:

• chr8-37094396-A-G
• chr8-37094396-A-T

Variant summary

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

The ENST00000744926.1(ENSG00000297043):​n.223-18284T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.1 in 152,290 control chromosomes in the GnomAD database, including 886 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 (886 hom., cov: 33)
• Consequence: ENSG00000297043 ENST00000744926.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.504
• Publications: 10 publications found

Genes affected

ENSG00000297043 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.239 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
ENSG00000297043	ENST00000744926.1	n.223-18284T>C		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.100 AC: 15214 AN: 152172 Hom.: 882 Cov.: 33

Gnomad AFR AF: 0.0914

Gnomad AMI AF: 0.0297

Gnomad AMR AF: 0.144

Gnomad ASJ AF: 0.100

Gnomad EAS AF: 0.251

Gnomad SAS AF: 0.106

Gnomad FIN AF: 0.108

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0832

Gnomad OTH AF: 0.0937

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

GnomAD4 genome AF: 0.100 AC: 15228 AN: 152290 Hom.: 886 Cov.: 33 AF XY: 0.103 AC XY: 7663 AN XY: 74470

African (AFR) AF: 0.0913 AC: 3796 AN: 41564

American (AMR) AF: 0.144 AC: 2208 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.100 AC: 348 AN: 3472

East Asian (EAS) AF: 0.251 AC: 1299 AN: 5182

South Asian (SAS) AF: 0.106 AC: 511 AN: 4820

European-Finnish (FIN) AF: 0.108 AC: 1149 AN: 10612

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.0832 AC: 5661 AN: 68028

Other (OTH) AF: 0.0951 AC: 201 AN: 2114

Alfa AF: 0.0885 Hom.: 1313

Bravo AF: 0.104

Asia WGS AF: 0.189 AC: 659 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.2
DANN	Benign	0.73
PhyloP100		0.50

Splicing

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

Other links and lift over

dbSNP: rs2407103; hg19: chr8-36951914;