rs4749080

Variant names:

• chr10-25873837-A-G
• rs4749080
• ENST00000744909.1:n.400-10501A>G

Variant summary

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

The ENST00000744909.1(ENSG00000297038):​n.400-10501A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.11 in 152,194 control chromosomes in the GnomAD database, including 1,205 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 (1205 hom., cov: 31)
• Consequence: ENSG00000297038 ENST00000744909.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.286
• Publications: 4 publications found

Genes affected

ENSG00000297038 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.279 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
ENSG00000297038	ENST00000744909.1	n.400-10501A>G		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.110 AC: 16717 AN: 152076 Hom.: 1205 Cov.: 31

Gnomad AFR AF: 0.0561

Gnomad AMI AF: 0.0954

Gnomad AMR AF: 0.181

Gnomad ASJ AF: 0.0838

Gnomad EAS AF: 0.291

Gnomad SAS AF: 0.160

Gnomad FIN AF: 0.165

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.103

Gnomad OTH AF: 0.0956

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

GnomAD4 genome AF: 0.110 AC: 16721 AN: 152194 Hom.: 1205 Cov.: 31 AF XY: 0.116 AC XY: 8655 AN XY: 74412

African (AFR) AF: 0.0560 AC: 2325 AN: 41532

American (AMR) AF: 0.181 AC: 2774 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0838 AC: 291 AN: 3472

East Asian (EAS) AF: 0.291 AC: 1501 AN: 5162

South Asian (SAS) AF: 0.161 AC: 775 AN: 4824

European-Finnish (FIN) AF: 0.165 AC: 1751 AN: 10586

Middle Eastern (MID) AF: 0.133 AC: 39 AN: 294

European-Non Finnish (NFE) AF: 0.103 AC: 6977 AN: 68006

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

Alfa AF: 0.105 Hom.: 1926

Bravo AF: 0.108

Asia WGS AF: 0.216 AC: 751 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.7
DANN	Benign	0.56
PhyloP100		0.29

Splicing

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

Other links and lift over

dbSNP: rs4749080; hg19: chr10-26162766;