rs2445234

Positions:

• chr2-128531089-G-A

Variant summary

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

The XR_923318.2(LOC105373611):​n.2388-90262G>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 0.219 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.120

Genes affected

LOC105373611 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
LOC105373611	XR_923318.2	n.2388-90262G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.559

Gnomad4 AMR AF: 0.143

Gnomad4 ASJ AF: 0.104

Gnomad4 EAS AF: 0.0315

Gnomad4 SAS AF: 0.0845

Gnomad4 FIN AF: 0.0562

Gnomad4 NFE AF: 0.0868

Gnomad4 OTH AF: 0.207

Alfa AF: 0.164 Hom.: 541

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2445234; hg19: chr2-129288663;