rs10049135

Variant names:

• chr3-72599829-A-G
• rs10049135
• ENST00000747314.1:n.850+1732T>C

Variant summary

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

The ENST00000747314.1(ENSG00000297356):​n.850+1732T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.159 in 152,068 control chromosomes in the GnomAD database, including 2,155 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 0.16 (2155 hom., cov: 32)
• Consequence: ENSG00000297356 ENST00000747314.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.55
• Publications: 0 publications found

Genes affected

ENSG00000297356 (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 = 0.345 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000747314.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000297356	ENST00000747314.1		n.850+1732T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.159 AC: 24203 AN: 151950 Hom.: 2148 Cov.: 32

Gnomad AFR AF: 0.180

Gnomad AMI AF: 0.165

Gnomad AMR AF: 0.214

Gnomad ASJ AF: 0.204

Gnomad EAS AF: 0.358

Gnomad SAS AF: 0.245

Gnomad FIN AF: 0.0837

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.122

Gnomad OTH AF: 0.181

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

GnomAD4 genome AF: 0.159 AC: 24227 AN: 152068 Hom.: 2155 Cov.: 32 AF XY: 0.162 AC XY: 12068 AN XY: 74326

African (AFR) AF: 0.180 AC: 7470 AN: 41462

American (AMR) AF: 0.214 AC: 3269 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.204 AC: 706 AN: 3464

East Asian (EAS) AF: 0.358 AC: 1847 AN: 5154

South Asian (SAS) AF: 0.243 AC: 1167 AN: 4804

European-Finnish (FIN) AF: 0.0837 AC: 886 AN: 10590

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

European-Non Finnish (NFE) AF: 0.122 AC: 8276 AN: 68004

Other (OTH) AF: 0.185 AC: 391 AN: 2110

Alfa AF: 0.144 Hom.: 3188

Bravo AF: 0.169

Asia WGS AF: 0.293 AC: 1019 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.084
DANN	Benign	0.32
PhyloP100		-2.5

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10049135;

hg19: chr3-72648980;