chr2-55862405-A-G

Position:

• chr2-55862405-A-G

Variant summary

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

The XR_002959388.2(LOC112268416):​n.229-11478A>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 0.658 in 152,000 control chromosomes in the GnomAD database, including 34,728 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 0.66 (34728 hom., cov: 31)
• Consequence: LOC112268416 XR_002959388.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.490

Genes affected

LOC112268416 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.878 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC112268416	XR_002959388.2	n.229-11478A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.658 AC: 99921 AN: 151882 Hom.: 34687 Cov.: 31

Gnomad AFR AF: 0.861

Gnomad AMI AF: 0.714

Gnomad AMR AF: 0.538

Gnomad ASJ AF: 0.736

Gnomad EAS AF: 0.899

Gnomad SAS AF: 0.682

Gnomad FIN AF: 0.440

Gnomad MID AF: 0.753

Gnomad NFE AF: 0.569

Gnomad OTH AF: 0.671

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

GnomAD4 genome AF: 0.658 AC: 100020 AN: 152000 Hom.: 34728 Cov.: 31 AF XY: 0.655 AC XY: 48630 AN XY: 74270

Gnomad4 AFR AF: 0.861

Gnomad4 AMR AF: 0.538

Gnomad4 ASJ AF: 0.736

Gnomad4 EAS AF: 0.899

Gnomad4 SAS AF: 0.683

Gnomad4 FIN AF: 0.440

Gnomad4 NFE AF: 0.569

Gnomad4 OTH AF: 0.674

Alfa AF: 0.615 Hom.: 13716

Bravo AF: 0.672

Asia WGS AF: 0.788 AC: 2740 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.1
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1367226; hg19: chr2-56089540;