rs10183748

Variant names:

• chr2-47970829-C-T
• rs10183748
• ENST00000447571.5:n.442-22420G>A

Variant summary

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

The ENST00000447571.5(ENSG00000230773):​n.442-22420G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.283 in 152,092 control chromosomes in the GnomAD database, including 7,355 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 0.28 (7355 hom., cov: 32)
• Consequence: ENSG00000230773 ENST00000447571.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.734
• Publications: 2 publications found

Genes affected

ENSG00000230773 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.373 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000447571.5. 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
	ENSG00000230773	ENST00000447571.5	TSL:1	n.442-22420G>A		intron	N/A
	ENSG00000230773	ENST00000587616.1	TSL:5	n.944-8253G>A		intron	N/A
	ENSG00000230773	ENST00000649883.1		n.403-22420G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.283 AC: 43058 AN: 151974 Hom.: 7353 Cov.: 32

Gnomad AFR AF: 0.111

Gnomad AMI AF: 0.355

Gnomad AMR AF: 0.293

Gnomad ASJ AF: 0.315

Gnomad EAS AF: 0.0654

Gnomad SAS AF: 0.299

Gnomad FIN AF: 0.418

Gnomad MID AF: 0.364

Gnomad NFE AF: 0.377

Gnomad OTH AF: 0.293

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

GnomAD4 genome AF: 0.283 AC: 43067 AN: 152092 Hom.: 7355 Cov.: 32 AF XY: 0.282 AC XY: 20981 AN XY: 74330

African (AFR) AF: 0.111 AC: 4608 AN: 41508

American (AMR) AF: 0.293 AC: 4484 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.315 AC: 1092 AN: 3470

East Asian (EAS) AF: 0.0654 AC: 338 AN: 5172

South Asian (SAS) AF: 0.300 AC: 1446 AN: 4824

European-Finnish (FIN) AF: 0.418 AC: 4408 AN: 10552

Middle Eastern (MID) AF: 0.367 AC: 108 AN: 294

European-Non Finnish (NFE) AF: 0.377 AC: 25636 AN: 67958

Other (OTH) AF: 0.295 AC: 624 AN: 2114

Alfa AF: 0.343 Hom.: 9728

Bravo AF: 0.263

Asia WGS AF: 0.173 AC: 600 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	11
DANN	Benign	0.45
PhyloP100		0.73

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: rs10183748;

hg19: chr2-48197968;