rs13410282

Positions:

• chr2-201106301-G-A

Variant summary

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

The XR_923785.3(LOC105373836):​n.1838-498C>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 0.307 in 151,958 control chromosomes in the GnomAD database, including 9,285 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 0.31 (9285 hom., cov: 32)
• Consequence: LOC105373836 XR_923785.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.136

Genes affected

LOC105373836 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.556 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105373836	XR_923785.3	n.1838-498C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.306 AC: 46525 AN: 151842 Hom.: 9261 Cov.: 32

Gnomad AFR AF: 0.562

Gnomad AMI AF: 0.178

Gnomad AMR AF: 0.205

Gnomad ASJ AF: 0.335

Gnomad EAS AF: 0.0135

Gnomad SAS AF: 0.144

Gnomad FIN AF: 0.205

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.225

Gnomad OTH AF: 0.280

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

GnomAD4 genome AF: 0.307 AC: 46608 AN: 151958 Hom.: 9285 Cov.: 32 AF XY: 0.302 AC XY: 22402 AN XY: 74274

Gnomad4 AFR AF: 0.562

Gnomad4 AMR AF: 0.205

Gnomad4 ASJ AF: 0.335

Gnomad4 EAS AF: 0.0135

Gnomad4 SAS AF: 0.143

Gnomad4 FIN AF: 0.205

Gnomad4 NFE AF: 0.225

Gnomad4 OTH AF: 0.286

Alfa AF: 0.248 Hom.: 5282

Bravo AF: 0.317

Asia WGS AF: 0.129 AC: 452 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.45
DANN	Benign	0.23

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13410282; hg19: chr2-201971024;