chr2-162136981-C-T

Position:

• chr2-162136981-C-T

Variant summary

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

The NR_110255.1(LOC101929532):​n.92+22449C>T 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 0.385 in 151,346 control chromosomes in the GnomAD database, including 11,913 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 0.38 (11913 hom., cov: 32)
• Consequence: LOC101929532 NR_110255.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0250

Genes affected

LOC101929532 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.684 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC101929532	NR_110255.1	n.92+22449C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.385 AC: 58239 AN: 151230 Hom.: 11912 Cov.: 32

Gnomad AFR AF: 0.264

Gnomad AMI AF: 0.474

Gnomad AMR AF: 0.369

Gnomad ASJ AF: 0.480

Gnomad EAS AF: 0.703

Gnomad SAS AF: 0.529

Gnomad FIN AF: 0.440

Gnomad MID AF: 0.453

Gnomad NFE AF: 0.413

Gnomad OTH AF: 0.380

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

GnomAD4 genome AF: 0.385 AC: 58265 AN: 151346 Hom.: 11913 Cov.: 32 AF XY: 0.391 AC XY: 28932 AN XY: 73918

Gnomad4 AFR AF: 0.264

Gnomad4 AMR AF: 0.369

Gnomad4 ASJ AF: 0.480

Gnomad4 EAS AF: 0.703

Gnomad4 SAS AF: 0.528

Gnomad4 FIN AF: 0.440

Gnomad4 NFE AF: 0.414

Gnomad4 OTH AF: 0.385

Alfa AF: 0.374 Hom.: 1366

Bravo AF: 0.375

Asia WGS AF: 0.549 AC: 1894 AN: 3450

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.4
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7599142; hg19: chr2-162993491;