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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105374591	XR_001739454.2	n.455+25887G>A		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000230773	ENST00000447571.5	n.442-22420G>A		intron_variant	Intron 5 of 8	1
ENSG00000230773	ENST00000587616.1	n.944-8253G>A		intron_variant	Intron 8 of 10	5
ENSG00000230773	ENST00000649883.1	n.403-22420G>A		intron_variant	Intron 5 of 8

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 v4.3

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

Other links and lift over

dbSNP: rs10183748; hg19: chr2-48197968;