2-156357858-G-A

Position:

• chr2-156357858-G-A

Variant summary

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

The XR_007088691.1(LOC124906082):​n.135-3134G>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 0.392 in 152,036 control chromosomes in the GnomAD database, including 13,966 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 0.39 (13966 hom., cov: 33)
• Consequence: LOC124906082 XR_007088691.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0200

Genes affected

LOC124906082 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.533 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124906082	XR_007088691.1	n.135-3134G>A		intron_variant, non_coding_transcript_variant
LOC124906082	XR_007088690.1	n.149+2550G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.392 AC: 59554 AN: 151918 Hom.: 13964 Cov.: 33

Gnomad AFR AF: 0.151

Gnomad AMI AF: 0.501

Gnomad AMR AF: 0.313

Gnomad ASJ AF: 0.475

Gnomad EAS AF: 0.195

Gnomad SAS AF: 0.429

Gnomad FIN AF: 0.555

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.538

Gnomad OTH AF: 0.396

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

GnomAD4 genome AF: 0.392 AC: 59552 AN: 152036 Hom.: 13966 Cov.: 33 AF XY: 0.388 AC XY: 28831 AN XY: 74310

Gnomad4 AFR AF: 0.151

Gnomad4 AMR AF: 0.313

Gnomad4 ASJ AF: 0.475

Gnomad4 EAS AF: 0.195

Gnomad4 SAS AF: 0.429

Gnomad4 FIN AF: 0.555

Gnomad4 NFE AF: 0.538

Gnomad4 OTH AF: 0.394

Alfa AF: 0.497 Hom.: 11667

Bravo AF: 0.356

Asia WGS AF: 0.297 AC: 1032 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	5.8
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs707132; hg19: chr2-157214370;