rs1822180

Variant names:

• chr2-234815484-G-A
• rs1822180
• XR_007088126.1:n.2323C>T

Your query was ambiguous. Multiple possible variants found:

• chr2-234815484-G-A
• chr2-234815484-G-C
• chr2-234815484-G-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_007088126.1(LOC101927896):​n.2323C>T variant causes a non coding transcript exon 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: LOC101927896 XR_007088126.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.233
• Publications: 2 publications found

Genes affected

LOC101927896 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LOC101927896	XR_007088126.1	n.2323C>T		non_coding_transcript_exon_variant	Exon 4 of 4
LOC101927896	XR_002959457.2	n.1253+1758C>T		intron_variant	Intron 6 of 8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000235726	ENST00000669419.1	n.611+1758C>T		intron_variant	Intron 5 of 5
ENSG00000235726	ENST00000825569.1	n.473+9449C>T		intron_variant	Intron 3 of 3
ENSG00000235726	ENST00000825570.1	n.274-21682C>T		intron_variant	Intron 2 of 2

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

African (AFR) AF: 0.368 AC: 15221 AN: 41402

American (AMR) AF: 0.533 AC: 8140 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.411 AC: 1423 AN: 3466

East Asian (EAS) AF: 0.489 AC: 2508 AN: 5134

South Asian (SAS) AF: 0.650 AC: 3120 AN: 4802

European-Finnish (FIN) AF: 0.519 AC: 5462 AN: 10532

Middle Eastern (MID) AF: 0.320 AC: 94 AN: 294

European-Non Finnish (NFE) AF: 0.447 AC: 30327 AN: 67920

Other (OTH) AF: 0.427 AC: 902 AN: 2110

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
PhyloP100		-0.23

Splicing

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

Other links and lift over

dbSNP: rs1822180; hg19: chr2-235724128;