2-42919660-T-C

Variant summary

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

The XR_940014.3(LOC105374568):n.2132A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.646 in 152,080 control chromosomes in the GnomAD database, including 32,605 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 0.65 (32605 hom., cov: 32)
• Consequence: LOC105374568 XR_940014.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.547

Genes affected

LOC105374568 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.762 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105374568	XR_940014.3	n.2132A>G		non_coding_transcript_exon_variant	3/3

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.646 AC: 98202 AN: 151962 Hom.: 32553 Cov.: 32

Gnomad AFR AF: 0.769

Gnomad AMI AF: 0.388

Gnomad AMR AF: 0.728

Gnomad ASJ AF: 0.661

Gnomad EAS AF: 0.650

Gnomad SAS AF: 0.748

Gnomad FIN AF: 0.558

Gnomad MID AF: 0.804

Gnomad NFE AF: 0.561

Gnomad OTH AF: 0.660

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

GnomAD4 genome AF: 0.646 AC: 98312 AN: 152080 Hom.: 32605 Cov.: 32 AF XY: 0.649 AC XY: 48251 AN XY: 74352

Gnomad4 AFR AF: 0.769

Gnomad4 AMR AF: 0.728

Gnomad4 ASJ AF: 0.661

Gnomad4 EAS AF: 0.651

Gnomad4 SAS AF: 0.748

Gnomad4 FIN AF: 0.558

Gnomad4 NFE AF: 0.561

Gnomad4 OTH AF: 0.664

Alfa AF: 0.607 Hom.: 12639

Bravo AF: 0.666

Asia WGS AF: 0.744 AC: 2587 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	3.2
Dann	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1078100; hg19: chr2-43146800;