rs10183748

Positions:

• chr2-47970829-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000651429.1(ENSG00000230773):​n.417-20566G>A variant causes a intron, non coding transcript 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: ENST00000651429.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.734

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
LOC105374591	XR_001739454.2	n.455+25887G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000447571.5	n.442-22420G>A		intron_variant, non_coding_transcript_variant		1
	ENST00000651429.1	n.417-20566G>A		intron_variant, non_coding_transcript_variant
	ENST00000587616.1	n.944-8253G>A		intron_variant, non_coding_transcript_variant		5
	ENST00000649883.1	n.403-22420G>A		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.111

Gnomad4 AMR AF: 0.293

Gnomad4 ASJ AF: 0.315

Gnomad4 EAS AF: 0.0654

Gnomad4 SAS AF: 0.300

Gnomad4 FIN AF: 0.418

Gnomad4 NFE AF: 0.377

Gnomad4 OTH AF: 0.295

Alfa AF: 0.348 Hom.: 5983

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10183748; hg19: chr2-48197968;