2-104681545-A-T

Position:

• chr2-104681545-A-T

Variant summary

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

The NR_188087.1(LOC105373526):​n.1124-3175A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.634 in 152,152 control chromosomes in the GnomAD database, including 34,250 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 0.63 (34250 hom., cov: 32)
• Consequence: LOC105373526 NR_188087.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.53

Genes affected

ENSG00000288565 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.79 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105373526	NR_188087.1	n.1124-3175A>T		intron_variant
LOC105373526	NR_188088.1	n.1168+1065A>T		intron_variant
LOC105373526	NR_188089.1	n.988+1065A>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000288565	ENST00000669335.1	n.4095-24542T>A		intron_variant

Frequencies

GnomAD3 genomes AF: 0.634 AC: 96391 AN: 152034 Hom.: 34250 Cov.: 32

Gnomad AFR AF: 0.294

Gnomad AMI AF: 0.952

Gnomad AMR AF: 0.653

Gnomad ASJ AF: 0.718

Gnomad EAS AF: 0.573

Gnomad SAS AF: 0.700

Gnomad FIN AF: 0.834

Gnomad MID AF: 0.699

Gnomad NFE AF: 0.796

Gnomad OTH AF: 0.673

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

GnomAD4 genome AF: 0.634 AC: 96389 AN: 152152 Hom.: 34250 Cov.: 32 AF XY: 0.635 AC XY: 47241 AN XY: 74378

Gnomad4 AFR AF: 0.293

Gnomad4 AMR AF: 0.652

Gnomad4 ASJ AF: 0.718

Gnomad4 EAS AF: 0.573

Gnomad4 SAS AF: 0.701

Gnomad4 FIN AF: 0.834

Gnomad4 NFE AF: 0.796

Gnomad4 OTH AF: 0.672

Alfa AF: 0.706 Hom.: 5047

Bravo AF: 0.603

Asia WGS AF: 0.614 AC: 2137 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	5.1
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1517853; hg19: chr2-105298003;