2-70557529-C-G

Position:

• chr2-70557529-C-G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The XR_007086906.1(LOC124907824):​n.685+4137C>G 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 0.228 in 152,120 control chromosomes in the GnomAD database, including 4,339 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 0.23 (4339 hom., cov: 32)
• Consequence: LOC124907824 XR_007086906.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.27

Genes affected

LOC124907824 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.25).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.297 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124907824	XR_007086906.1	n.685+4137C>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.228 AC: 34626 AN: 152002 Hom.: 4318 Cov.: 32

Gnomad AFR AF: 0.301

Gnomad AMI AF: 0.259

Gnomad AMR AF: 0.162

Gnomad ASJ AF: 0.214

Gnomad EAS AF: 0.288

Gnomad SAS AF: 0.254

Gnomad FIN AF: 0.170

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.201

Gnomad OTH AF: 0.219

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

GnomAD4 genome AF: 0.228 AC: 34676 AN: 152120 Hom.: 4339 Cov.: 32 AF XY: 0.226 AC XY: 16811 AN XY: 74356

Gnomad4 AFR AF: 0.301

Gnomad4 AMR AF: 0.162

Gnomad4 ASJ AF: 0.214

Gnomad4 EAS AF: 0.288

Gnomad4 SAS AF: 0.253

Gnomad4 FIN AF: 0.170

Gnomad4 NFE AF: 0.201

Gnomad4 OTH AF: 0.221

Alfa AF: 0.102 Hom.: 160

Bravo AF: 0.229

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.25
CADD	Benign	16
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13392762; hg19: chr2-70784661;