chr5-12383830-G-A

Variant names:

• chr5-12383830-G-A
• rs7712169
• ENST00000830573.1:n.472-15836C>T

Variant summary

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

The ENST00000830573.1(ENSG00000248783):​n.472-15836C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0575 in 152,092 control chromosomes in the GnomAD database, including 528 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 0.058 (528 hom., cov: 32)
• Consequence: ENSG00000248783 ENST00000830573.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.611
• Publications: 2 publications found

Genes affected

ENSG00000248783 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.148 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105374655	NR_188266.1	n.366-15836C>T		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000248783	ENST00000830573.1	n.472-15836C>T		intron_variant	Intron 3 of 5
ENSG00000248783	ENST00000830574.1	n.491-15836C>T		intron_variant	Intron 3 of 4
ENSG00000248783	ENST00000830575.1	n.588-15836C>T		intron_variant	Intron 4 of 5

Frequencies

GnomAD3 genomes AF: 0.0575 AC: 8737 AN: 151972 Hom.: 526 Cov.: 32

Gnomad AFR AF: 0.151

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0329

Gnomad ASJ AF: 0.0222

Gnomad EAS AF: 0.00116

Gnomad SAS AF: 0.0788

Gnomad FIN AF: 0.0136

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0188

Gnomad OTH AF: 0.0522

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

GnomAD4 genome AF: 0.0575 AC: 8750 AN: 152092 Hom.: 528 Cov.: 32 AF XY: 0.0568 AC XY: 4225 AN XY: 74338

African (AFR) AF: 0.151 AC: 6254 AN: 41448

American (AMR) AF: 0.0328 AC: 501 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0222 AC: 77 AN: 3468

East Asian (EAS) AF: 0.00116 AC: 6 AN: 5170

South Asian (SAS) AF: 0.0780 AC: 376 AN: 4818

European-Finnish (FIN) AF: 0.0136 AC: 144 AN: 10584

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.0187 AC: 1275 AN: 68010

Other (OTH) AF: 0.0516 AC: 109 AN: 2112

Alfa AF: 0.0342 Hom.: 479

Bravo AF: 0.0614

Asia WGS AF: 0.0390 AC: 134 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.21
DANN	Benign	0.35
PhyloP100		-0.61

Splicing

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

Other links and lift over

dbSNP: rs7712169; hg19: chr5-12383942;