XM_047433430.1:c.2184+814G>C

Variant names:

• chr15-73379176-G-C
• rs3940418
• XM_047433430.1:c.2184+814G>C

Variant summary

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

The XM_047433430.1(LOC124903571):​c.2184+814G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.104 in 152,250 control chromosomes in the GnomAD database, including 1,019 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 0.10 (1019 hom., cov: 33)
• Consequence: LOC124903571 XM_047433430.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0390
• Publications: 5 publications found

Genes affected

LOC124903571 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.154 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: 0.104 AC: 15873 AN: 152132 Hom.: 1012 Cov.: 33

Gnomad AFR AF: 0.157

Gnomad AMI AF: 0.109

Gnomad AMR AF: 0.113

Gnomad ASJ AF: 0.0789

Gnomad EAS AF: 0.0129

Gnomad SAS AF: 0.0656

Gnomad FIN AF: 0.142

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.0758

Gnomad OTH AF: 0.0908

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

GnomAD4 genome AF: 0.104 AC: 15903 AN: 152250 Hom.: 1019 Cov.: 33 AF XY: 0.106 AC XY: 7897 AN XY: 74436

African (AFR) AF: 0.157 AC: 6526 AN: 41542

American (AMR) AF: 0.114 AC: 1742 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0789 AC: 274 AN: 3472

East Asian (EAS) AF: 0.0133 AC: 69 AN: 5182

South Asian (SAS) AF: 0.0651 AC: 314 AN: 4826

European-Finnish (FIN) AF: 0.142 AC: 1509 AN: 10598

Middle Eastern (MID) AF: 0.0918 AC: 27 AN: 294

European-Non Finnish (NFE) AF: 0.0758 AC: 5154 AN: 68010

Other (OTH) AF: 0.0894 AC: 189 AN: 2114

Alfa AF: 0.101 Hom.: 101

Bravo AF: 0.104

Asia WGS AF: 0.0510 AC: 179 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.5
DANN	Benign	0.60
PhyloP100		-0.039

Splicing

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

Other links and lift over

dbSNP: rs3940418; hg19: chr15-73671517;