rs2467350

Positions:

• chr15-36480608-A-C

Variant summary

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

The XR_932110.1(LOC105370768):​n.249-4310A>C 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 0.35 in 152,110 control chromosomes in the GnomAD database, including 9,484 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 0.35 (9484 hom., cov: 32)
• Consequence: LOC105370768 XR_932110.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.274

Genes affected

LOC105370768 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.461 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105370768	XR_932110.1	n.249-4310A>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.350 AC: 53238 AN: 151990 Hom.: 9471 Cov.: 32

Gnomad AFR AF: 0.327

Gnomad AMI AF: 0.329

Gnomad AMR AF: 0.470

Gnomad ASJ AF: 0.378

Gnomad EAS AF: 0.321

Gnomad SAS AF: 0.251

Gnomad FIN AF: 0.379

Gnomad MID AF: 0.324

Gnomad NFE AF: 0.341

Gnomad OTH AF: 0.379

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

GnomAD4 genome AF: 0.350 AC: 53283 AN: 152110 Hom.: 9484 Cov.: 32 AF XY: 0.352 AC XY: 26150 AN XY: 74344

Gnomad4 AFR AF: 0.326

Gnomad4 AMR AF: 0.471

Gnomad4 ASJ AF: 0.378

Gnomad4 EAS AF: 0.321

Gnomad4 SAS AF: 0.252

Gnomad4 FIN AF: 0.379

Gnomad4 NFE AF: 0.341

Gnomad4 OTH AF: 0.380

Alfa AF: 0.343 Hom.: 18541

Bravo AF: 0.359

Asia WGS AF: 0.347 AC: 1206 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	6.9
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2467350; hg19: chr15-36772809;