15-73641377-A-G

Variant names:

• chr15-73641377-A-G
• rs1564492
• XR_932451.3:n.321+4640A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_932451.3(LOC105370891):​n.321+4640A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0958 in 152,186 control chromosomes in the GnomAD database, including 889 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 0.096 (889 hom., cov: 32)
• Consequence: LOC105370891 XR_932451.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.12
• Publications: 8 publications found

Genes affected

LOC105370891 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.16 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: 0.0956 AC: 14544 AN: 152068 Hom.: 883 Cov.: 32

Gnomad AFR AF: 0.163

Gnomad AMI AF: 0.0143

Gnomad AMR AF: 0.0775

Gnomad ASJ AF: 0.0501

Gnomad EAS AF: 0.135

Gnomad SAS AF: 0.120

Gnomad FIN AF: 0.0719

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0616

Gnomad OTH AF: 0.0803

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

GnomAD4 genome AF: 0.0958 AC: 14576 AN: 152186 Hom.: 889 Cov.: 32 AF XY: 0.0966 AC XY: 7185 AN XY: 74406

African (AFR) AF: 0.164 AC: 6786 AN: 41496

American (AMR) AF: 0.0775 AC: 1186 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0501 AC: 174 AN: 3472

East Asian (EAS) AF: 0.136 AC: 699 AN: 5156

South Asian (SAS) AF: 0.120 AC: 579 AN: 4830

European-Finnish (FIN) AF: 0.0719 AC: 763 AN: 10606

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.0616 AC: 4192 AN: 68012

Other (OTH) AF: 0.0814 AC: 172 AN: 2114

Alfa AF: 0.0712 Hom.: 2065

Bravo AF: 0.0983

Asia WGS AF: 0.148 AC: 512 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	8.7
DANN	Benign	0.58
PhyloP100		2.1

Splicing

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

Other links and lift over

dbSNP: rs1564492; hg19: chr15-73933718;