rs4293326

Positions:

• chr15-66843706-G-A
• chr15-66843706-G-C

Variant summary

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

The XR_932381.3(LOC105376718):​n.837G>A 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 0.353 in 152,056 control chromosomes in the GnomAD database, including 10,844 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 (10844 hom., cov: 32)
• Consequence: LOC105376718 XR_932381.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.32

Genes affected

LOC105376718 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.548 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105376718	XR_932381.3	n.837G>A		non_coding_transcript_exon_variant	1/2

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.353 AC: 53641 AN: 151938 Hom.: 10798 Cov.: 32

Gnomad AFR AF: 0.553

Gnomad AMI AF: 0.0800

Gnomad AMR AF: 0.373

Gnomad ASJ AF: 0.255

Gnomad EAS AF: 0.257

Gnomad SAS AF: 0.281

Gnomad FIN AF: 0.214

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.271

Gnomad OTH AF: 0.330

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

GnomAD4 genome AF: 0.353 AC: 53745 AN: 152056 Hom.: 10844 Cov.: 32 AF XY: 0.350 AC XY: 26026 AN XY: 74314

Gnomad4 AFR AF: 0.554

Gnomad4 AMR AF: 0.374

Gnomad4 ASJ AF: 0.255

Gnomad4 EAS AF: 0.258

Gnomad4 SAS AF: 0.280

Gnomad4 FIN AF: 0.214

Gnomad4 NFE AF: 0.271

Gnomad4 OTH AF: 0.330

Alfa AF: 0.322 Hom.: 2938

Bravo AF: 0.374

Asia WGS AF: 0.303 AC: 1055 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.0030
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4293326; hg19: chr15-67136044;