2-13628292-T-G

Variant summary

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

The XR_922816.2(LOC105373438):n.104+19131T>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 0.791 in 151,898 control chromosomes in the GnomAD database, including 48,999 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 0.79 (48999 hom., cov: 31)
• Consequence: LOC105373438 XR_922816.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0480

Genes affected

LOC105373438 (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 (NFE) allele frequency at 95% confidence interval = 0.902 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105373438	XR_922816.2	n.104+19131T>G		intron_variant, non_coding_transcript_variant
LOC105373438	XR_922815.2	n.104+19131T>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.792 AC: 120149 AN: 151778 Hom.: 48992 Cov.: 31

Gnomad AFR AF: 0.643

Gnomad AMI AF: 0.954

Gnomad AMR AF: 0.755

Gnomad ASJ AF: 0.885

Gnomad EAS AF: 0.400

Gnomad SAS AF: 0.746

Gnomad FIN AF: 0.839

Gnomad MID AF: 0.835

Gnomad NFE AF: 0.908

Gnomad OTH AF: 0.807

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

GnomAD4 genome AF: 0.791 AC: 120212 AN: 151898 Hom.: 48999 Cov.: 31 AF XY: 0.784 AC XY: 58228 AN XY: 74252

Gnomad4 AFR AF: 0.643

Gnomad4 AMR AF: 0.755

Gnomad4 ASJ AF: 0.885

Gnomad4 EAS AF: 0.400

Gnomad4 SAS AF: 0.745

Gnomad4 FIN AF: 0.839

Gnomad4 NFE AF: 0.908

Gnomad4 OTH AF: 0.806

Alfa AF: 0.845 Hom.: 6844

Bravo AF: 0.777

Asia WGS AF: 0.625 AC: 2173 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	1.7
Dann	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1510823; hg19: chr2-13768417;