chr15-66843706-G-A

Variant names:

• chr15-66843706-G-A
• rs4293326
• XR_932381.3:n.837G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

Genes affected

LOC105376718 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.554 AC: 22953 AN: 41468

American (AMR) AF: 0.374 AC: 5708 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.255 AC: 884 AN: 3468

East Asian (EAS) AF: 0.258 AC: 1331 AN: 5168

South Asian (SAS) AF: 0.280 AC: 1348 AN: 4814

European-Finnish (FIN) AF: 0.214 AC: 2258 AN: 10574

Middle Eastern (MID) AF: 0.241 AC: 71 AN: 294

European-Non Finnish (NFE) AF: 0.271 AC: 18422 AN: 67970

Other (OTH) AF: 0.330 AC: 697 AN: 2110

Alfa AF: 0.321 Hom.: 3532

Bravo AF: 0.374

Asia WGS AF: 0.303 AC: 1055 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.0030
DANN	Benign	0.49
PhyloP100		-3.3

Splicing

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

Other links and lift over

dbSNP: rs4293326; hg19: chr15-67136044;