rs1822180

chr2-234815484-G-Achr2-234815484-G-Cchr2-234815484-G-T

Variant summary

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

The ENST00000669419.1(ENSG00000235726):n.611+1758C>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 0.445 in 151,832 control chromosomes in the GnomAD database, including 15,396 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 0.45 (15396 hom., cov: 31)
• Consequence: ENST00000669419.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.233

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.631 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC101927896	XR_002959457.2	n.1253+1758C>T		intron_variant, non_coding_transcript_variant
LOC101927896	XR_007088126.1	n.2323C>T		non_coding_transcript_exon_variant	4/4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000669419.1	n.611+1758C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.446 AC: 67629 AN: 151716 Hom.: 15393 Cov.: 31

Gnomad AFR AF: 0.368

Gnomad AMI AF: 0.487

Gnomad AMR AF: 0.533

Gnomad ASJ AF: 0.411

Gnomad EAS AF: 0.488

Gnomad SAS AF: 0.650

Gnomad FIN AF: 0.519

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.446

Gnomad OTH AF: 0.430

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

GnomAD4 genome AF: 0.445 AC: 67640 AN: 151832 Hom.: 15396 Cov.: 31 AF XY: 0.453 AC XY: 33621 AN XY: 74172

Gnomad4 AFR AF: 0.368

Gnomad4 AMR AF: 0.533

Gnomad4 ASJ AF: 0.411

Gnomad4 EAS AF: 0.489

Gnomad4 SAS AF: 0.650

Gnomad4 FIN AF: 0.519

Gnomad4 NFE AF: 0.447

Gnomad4 OTH AF: 0.427

Alfa AF: 0.311 Hom.: 807

Bravo AF: 0.437

Asia WGS AF: 0.547 AC: 1903 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	1.3
Dann	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1822180; hg19: chr2-235724128;