10-47092629-C-G

Variant names:

• chr10-47092629-C-G
• rs733488
• ENST00000747950.1:n.84-523G>C

Variant summary

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

The ENST00000747950.1(ENSG00000297443):​n.84-523G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.295 in 152,188 control chromosomes in the GnomAD database, including 8,409 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 0.30 (8409 hom., cov: 33)
• Consequence: ENSG00000297443 ENST00000747950.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.842
• Publications: 2 publications found

Genes affected

ENSG00000297443 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.408 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000747950.1. 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
	ENSG00000297443	ENST00000747950.1		n.84-523G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.295 AC: 44929 AN: 152070 Hom.: 8403 Cov.: 33

Gnomad AFR AF: 0.0985

Gnomad AMI AF: 0.271

Gnomad AMR AF: 0.402

Gnomad ASJ AF: 0.501

Gnomad EAS AF: 0.00231

Gnomad SAS AF: 0.134

Gnomad FIN AF: 0.302

Gnomad MID AF: 0.350

Gnomad NFE AF: 0.412

Gnomad OTH AF: 0.344

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

GnomAD4 genome AF: 0.295 AC: 44948 AN: 152188 Hom.: 8409 Cov.: 33 AF XY: 0.287 AC XY: 21376 AN XY: 74400

African (AFR) AF: 0.0985 AC: 4091 AN: 41554

American (AMR) AF: 0.403 AC: 6155 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.501 AC: 1740 AN: 3470

East Asian (EAS) AF: 0.00232 AC: 12 AN: 5180

South Asian (SAS) AF: 0.136 AC: 656 AN: 4818

European-Finnish (FIN) AF: 0.302 AC: 3205 AN: 10598

Middle Eastern (MID) AF: 0.353 AC: 103 AN: 292

European-Non Finnish (NFE) AF: 0.412 AC: 28019 AN: 67958

Other (OTH) AF: 0.340 AC: 720 AN: 2116

Alfa AF: 0.346 Hom.: 1264

Bravo AF: 0.300

Asia WGS AF: 0.0870 AC: 302 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.53
DANN	Benign	0.44
PhyloP100		-0.84

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: rs733488;

hg19: chr10-48646733;