chr2-128531089-G-A

Variant names:

• chr2-128531089-G-A
• rs2445234
• XR_923318.2:n.2388-90262G>A

Variant summary

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

The XR_923318.2(LOC105373611):​n.2388-90262G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.219 in 152,146 control chromosomes in the GnomAD database, including 7,069 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 0.22 (7069 hom., cov: 32)
• Consequence: LOC105373611 XR_923318.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.120
• Publications: 1 publications found

Genes affected

LOC105373611 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.553 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105373611	XR_923318.2	n.2388-90262G>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.219 AC: 33225 AN: 152028 Hom.: 7036 Cov.: 32

Gnomad AFR AF: 0.558

Gnomad AMI AF: 0.0274

Gnomad AMR AF: 0.144

Gnomad ASJ AF: 0.104

Gnomad EAS AF: 0.0320

Gnomad SAS AF: 0.0838

Gnomad FIN AF: 0.0562

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.0868

Gnomad OTH AF: 0.209

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

GnomAD4 genome AF: 0.219 AC: 33320 AN: 152146 Hom.: 7069 Cov.: 32 AF XY: 0.213 AC XY: 15834 AN XY: 74404

African (AFR) AF: 0.559 AC: 23180 AN: 41466

American (AMR) AF: 0.143 AC: 2192 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.104 AC: 362 AN: 3468

East Asian (EAS) AF: 0.0315 AC: 163 AN: 5172

South Asian (SAS) AF: 0.0845 AC: 408 AN: 4828

European-Finnish (FIN) AF: 0.0562 AC: 596 AN: 10600

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.0868 AC: 5907 AN: 68014

Other (OTH) AF: 0.207 AC: 436 AN: 2108

Alfa AF: 0.180 Hom.: 671

Bravo AF: 0.240

Asia WGS AF: 0.111 AC: 386 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	3.3
DANN	Benign	0.46
PhyloP100		-0.12

Splicing

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

Other links and lift over

dbSNP: rs2445234; hg19: chr2-129288663;