rs12516844

Variant names:

• chr5-68742250-T-G
• rs12516844
• ENST00000507733.3:n.313+3203A>C

Variant summary

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

The ENST00000507733.3(ENSG00000248884):​n.313+3203A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.103 in 152,040 control chromosomes in the GnomAD database, including 937 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 (937 hom., cov: 32)
• Consequence: ENSG00000248884 ENST00000507733.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.151
• Publications: 3 publications found

Genes affected

ENSG00000248884 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.255 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105379013	XR_007058804.1	n.440+86458A>C		intron_variant	Intron 2 of 4
LOC105379013	XR_007058805.1	n.110+17338A>C		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000248884	ENST00000507733.3	n.313+3203A>C		intron_variant	Intron 2 of 5	2
ENSG00000248884	ENST00000688207.1	n.65+17338A>C		intron_variant	Intron 1 of 2
ENSG00000248884	ENST00000717704.1	n.110+17338A>C		intron_variant	Intron 1 of 6

Frequencies

GnomAD3 genomes AF: 0.103 AC: 15624 AN: 151920 Hom.: 937 Cov.: 32

Gnomad AFR AF: 0.0618

Gnomad AMI AF: 0.130

Gnomad AMR AF: 0.147

Gnomad ASJ AF: 0.135

Gnomad EAS AF: 0.267

Gnomad SAS AF: 0.130

Gnomad FIN AF: 0.0926

Gnomad MID AF: 0.157

Gnomad NFE AF: 0.102

Gnomad OTH AF: 0.122

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

GnomAD4 genome AF: 0.103 AC: 15640 AN: 152040 Hom.: 937 Cov.: 32 AF XY: 0.104 AC XY: 7704 AN XY: 74326

African (AFR) AF: 0.0619 AC: 2568 AN: 41510

American (AMR) AF: 0.147 AC: 2243 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.135 AC: 469 AN: 3466

East Asian (EAS) AF: 0.267 AC: 1369 AN: 5126

South Asian (SAS) AF: 0.132 AC: 633 AN: 4802

European-Finnish (FIN) AF: 0.0926 AC: 981 AN: 10596

Middle Eastern (MID) AF: 0.169 AC: 49 AN: 290

European-Non Finnish (NFE) AF: 0.102 AC: 6956 AN: 67952

Other (OTH) AF: 0.120 AC: 253 AN: 2112

Alfa AF: 0.105 Hom.: 2763

Bravo AF: 0.108

Asia WGS AF: 0.159 AC: 552 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.7
DANN	Benign	0.84
PhyloP100		0.15

Splicing

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

Other links and lift over

dbSNP: rs12516844; hg19: chr5-68038077;