12-3365479-A-C

Position:

• chr12-3365479-A-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_148995.1(LOC100128253):​n.64+580T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.163 in 152,230 control chromosomes in the GnomAD database, including 2,283 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 0.16 (2283 hom., cov: 33)
• Consequence: LOC100128253 NR_148995.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.362

Genes affected

ENSG00000291189 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.179 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC100128253	NR_148995.1	n.64+580T>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000291189	ENST00000636557.1	n.64+580T>G		intron_variant		5
ENSG00000291189	ENST00000637529.1	n.54+580T>G		intron_variant		5
ENSG00000291189	ENST00000685534.1	n.46+580T>G		intron_variant

Frequencies

GnomAD3 genomes AF: 0.163 AC: 24849 AN: 152112 Hom.: 2280 Cov.: 33

Gnomad AFR AF: 0.183

Gnomad AMI AF: 0.170

Gnomad AMR AF: 0.127

Gnomad ASJ AF: 0.317

Gnomad EAS AF: 0.000965

Gnomad SAS AF: 0.0903

Gnomad FIN AF: 0.202

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.163

Gnomad OTH AF: 0.173

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

GnomAD4 genome AF: 0.163 AC: 24882 AN: 152230 Hom.: 2283 Cov.: 33 AF XY: 0.161 AC XY: 11981 AN XY: 74426

Gnomad4 AFR AF: 0.183

Gnomad4 AMR AF: 0.127

Gnomad4 ASJ AF: 0.317

Gnomad4 EAS AF: 0.000967

Gnomad4 SAS AF: 0.0912

Gnomad4 FIN AF: 0.202

Gnomad4 NFE AF: 0.163

Gnomad4 OTH AF: 0.172

Alfa AF: 0.165 Hom.: 2955

Bravo AF: 0.161

Asia WGS AF: 0.0480 AC: 169 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	6.2
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs887357; hg19: chr12-3474645;