rs12972202

Variant names:

• chr19-52966751-T-G
• rs12972202
• ENST00000600068.1:n.489+3873A>C

Variant summary

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

The ENST00000600068.1(ENSG00000269082):​n.489+3873A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.172 in 151,820 control chromosomes in the GnomAD database, including 2,784 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 0.17 (2784 hom., cov: 31)
• Consequence: ENSG00000269082 ENST00000600068.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.91
• Publications: 1 publications found

Genes affected

ENSG00000269082 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.313 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000269082	ENST00000600068.1	n.489+3873A>C		intron_variant	Intron 3 of 3	4
ENSG00000306352	ENST00000817153.1	n.242+3454T>G		intron_variant	Intron 1 of 1
ZNF702P	ENST00000652240.1	n.*145A>C		downstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.172 AC: 26123 AN: 151702 Hom.: 2784 Cov.: 31

Gnomad AFR AF: 0.291

Gnomad AMI AF: 0.0493

Gnomad AMR AF: 0.139

Gnomad ASJ AF: 0.148

Gnomad EAS AF: 0.327

Gnomad SAS AF: 0.0911

Gnomad FIN AF: 0.0956

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.116

Gnomad OTH AF: 0.176

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

GnomAD4 genome AF: 0.172 AC: 26155 AN: 151820 Hom.: 2784 Cov.: 31 AF XY: 0.171 AC XY: 12683 AN XY: 74182

African (AFR) AF: 0.291 AC: 12019 AN: 41326

American (AMR) AF: 0.139 AC: 2124 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.148 AC: 513 AN: 3464

East Asian (EAS) AF: 0.326 AC: 1680 AN: 5152

South Asian (SAS) AF: 0.0908 AC: 438 AN: 4824

European-Finnish (FIN) AF: 0.0956 AC: 1008 AN: 10542

Middle Eastern (MID) AF: 0.190 AC: 56 AN: 294

European-Non Finnish (NFE) AF: 0.116 AC: 7901 AN: 67946

Other (OTH) AF: 0.176 AC: 371 AN: 2106

Alfa AF: 0.144 Hom.: 333

Bravo AF: 0.182

Asia WGS AF: 0.217 AC: 756 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	5.2
DANN	Benign	0.52
PhyloP100		1.9

Splicing

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

Other links and lift over

dbSNP: rs12972202; hg19: chr19-53470004;