chr2-184362344-C-T

Position:

• chr2-184362344-C-T

Variant summary

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

The ENST00000671393.1(ENSG00000286980):​n.550-17814C>T 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 0.487 in 151,868 control chromosomes in the GnomAD database, including 19,909 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 0.49 (19909 hom., cov: 32)
• Consequence: ENST00000671393.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.12

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.874 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC102724340	XR_001739819.1	n.318+29451C>T		intron_variant, non_coding_transcript_variant
LOC105373776	XR_923650.3	n.133-1951G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000671393.1	n.550-17814C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.487 AC: 73918 AN: 151748 Hom.: 19891 Cov.: 32

Gnomad AFR AF: 0.267

Gnomad AMI AF: 0.450

Gnomad AMR AF: 0.584

Gnomad ASJ AF: 0.489

Gnomad EAS AF: 0.895

Gnomad SAS AF: 0.603

Gnomad FIN AF: 0.622

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.539

Gnomad OTH AF: 0.487

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

GnomAD4 genome AF: 0.487 AC: 73957 AN: 151868 Hom.: 19909 Cov.: 32 AF XY: 0.494 AC XY: 36680 AN XY: 74232

Gnomad4 AFR AF: 0.266

Gnomad4 AMR AF: 0.585

Gnomad4 ASJ AF: 0.489

Gnomad4 EAS AF: 0.896

Gnomad4 SAS AF: 0.603

Gnomad4 FIN AF: 0.622

Gnomad4 NFE AF: 0.540

Gnomad4 OTH AF: 0.493

Alfa AF: 0.530 Hom.: 29130

Bravo AF: 0.478

Asia WGS AF: 0.717 AC: 2488 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.094
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1443022; hg19: chr2-185227071;