rs12332121

Variant names:

• chr5-116768100-C-G
• rs12332121
• ENST00000835801.1:n.183+3519C>G

Variant summary

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

The ENST00000835801.1(ENSG00000308692):​n.183+3519C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.2 in 152,096 control chromosomes in the GnomAD database, including 3,621 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 0.20 (3621 hom., cov: 31)
• Consequence: ENSG00000308692 ENST00000835801.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.152
• Publications: 5 publications found

Genes affected

ENSG00000308692 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.262 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105379133	XR_948689.3	n.148+3519C>G		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000308692	ENST00000835801.1	n.183+3519C>G		intron_variant	Intron 1 of 3
ENSG00000308692	ENST00000835802.1	n.183+3519C>G		intron_variant	Intron 1 of 4
ENSG00000308692	ENST00000835803.1	n.183+3519C>G		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.200 AC: 30444 AN: 151978 Hom.: 3621 Cov.: 31

Gnomad AFR AF: 0.0905

Gnomad AMI AF: 0.171

Gnomad AMR AF: 0.156

Gnomad ASJ AF: 0.261

Gnomad EAS AF: 0.109

Gnomad SAS AF: 0.274

Gnomad FIN AF: 0.329

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.256

Gnomad OTH AF: 0.203

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

GnomAD4 genome AF: 0.200 AC: 30438 AN: 152096 Hom.: 3621 Cov.: 31 AF XY: 0.202 AC XY: 15036 AN XY: 74340

African (AFR) AF: 0.0903 AC: 3750 AN: 41516

American (AMR) AF: 0.156 AC: 2382 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.261 AC: 906 AN: 3468

East Asian (EAS) AF: 0.108 AC: 562 AN: 5180

South Asian (SAS) AF: 0.274 AC: 1324 AN: 4824

European-Finnish (FIN) AF: 0.329 AC: 3466 AN: 10528

Middle Eastern (MID) AF: 0.170 AC: 50 AN: 294

European-Non Finnish (NFE) AF: 0.256 AC: 17417 AN: 67978

Other (OTH) AF: 0.202 AC: 425 AN: 2108

Alfa AF: 0.236 Hom.: 589

Bravo AF: 0.178

Asia WGS AF: 0.158 AC: 546 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	6.0
DANN	Benign	0.22
PhyloP100		0.15

Splicing

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

Other links and lift over

dbSNP: rs12332121; hg19: chr5-116103796;