rs12213703

Variant names:

• chr6-22821721-G-A
• rs12213703
• ENST00000420572.2:n.198-76653C>T

Variant summary

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

The ENST00000420572.2(ENSG00000233358):​n.198-76653C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0786 in 152,270 control chromosomes in the GnomAD database, including 574 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 0.079 (574 hom., cov: 33)
• Consequence: ENSG00000233358 ENST00000420572.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.835
• Publications: 3 publications found

Genes affected

ENSG00000233358 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.1 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
ENSG00000233358	ENST00000420572.2	n.198-76653C>T		intron_variant	Intron 2 of 2	3

Frequencies

GnomAD3 genomes AF: 0.0786 AC: 11961 AN: 152152 Hom.: 575 Cov.: 33

Gnomad AFR AF: 0.0468

Gnomad AMI AF: 0.0910

Gnomad AMR AF: 0.0726

Gnomad ASJ AF: 0.0882

Gnomad EAS AF: 0.00828

Gnomad SAS AF: 0.0703

Gnomad FIN AF: 0.0938

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.102

Gnomad OTH AF: 0.0775

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

GnomAD4 genome AF: 0.0786 AC: 11962 AN: 152270 Hom.: 574 Cov.: 33 AF XY: 0.0775 AC XY: 5773 AN XY: 74464

African (AFR) AF: 0.0467 AC: 1940 AN: 41570

American (AMR) AF: 0.0724 AC: 1108 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0882 AC: 306 AN: 3468

East Asian (EAS) AF: 0.00830 AC: 43 AN: 5182

South Asian (SAS) AF: 0.0708 AC: 342 AN: 4832

European-Finnish (FIN) AF: 0.0938 AC: 994 AN: 10602

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.102 AC: 6956 AN: 67998

Other (OTH) AF: 0.0786 AC: 166 AN: 2112

Alfa AF: 0.0928 Hom.: 841

Bravo AF: 0.0763

Asia WGS AF: 0.0410 AC: 141 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.072
DANN	Benign	0.59
PhyloP100		-0.83

Splicing

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

Other links and lift over

dbSNP: rs12213703; hg19: chr6-22821950;