rs1443021

Positions:

• chr2-184362257-T-A
• chr2-184362257-T-C

Variant summary

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

The ENST00000671393.1(ENSG00000286980):​n.550-17901T>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 0.649 in 151,914 control chromosomes in the GnomAD database, including 33,867 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 0.65 (33867 hom., cov: 32)
• Consequence: ENST00000671393.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.245

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.914 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC102724340	XR_001739819.1	n.318+29364T>A		intron_variant, non_coding_transcript_variant
LOC105373776	XR_923650.3	n.133-1864A>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000671393.1	n.550-17901T>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.649 AC: 98511 AN: 151796 Hom.: 33841 Cov.: 32

Gnomad AFR AF: 0.412

Gnomad AMI AF: 0.498

Gnomad AMR AF: 0.710

Gnomad ASJ AF: 0.720

Gnomad EAS AF: 0.937

Gnomad SAS AF: 0.785

Gnomad FIN AF: 0.781

Gnomad MID AF: 0.671

Gnomad NFE AF: 0.726

Gnomad OTH AF: 0.640

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

GnomAD4 genome AF: 0.649 AC: 98576 AN: 151914 Hom.: 33867 Cov.: 32 AF XY: 0.654 AC XY: 48554 AN XY: 74254

Gnomad4 AFR AF: 0.413

Gnomad4 AMR AF: 0.710

Gnomad4 ASJ AF: 0.720

Gnomad4 EAS AF: 0.937

Gnomad4 SAS AF: 0.787

Gnomad4 FIN AF: 0.781

Gnomad4 NFE AF: 0.726

Gnomad4 OTH AF: 0.643

Alfa AF: 0.676 Hom.: 4426

Bravo AF: 0.633

Asia WGS AF: 0.836 AC: 2900 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.2
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1443021; hg19: chr2-185226984;