rs12202284

Variant names:

• chr6-471136-C-A
• rs12202284
• ENST00000661640.1:n.336-4072C>A

Your query was ambiguous. Multiple possible variants found:

• chr6-471136-C-A
• chr6-471136-C-T

Variant summary

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

The ENST00000661640.1(ENSG00000286364):​n.336-4072C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.198 in 152,184 control chromosomes in the GnomAD database, including 3,355 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 (3355 hom., cov: 33)
• Consequence: ENSG00000286364 ENST00000661640.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.172

Genes affected

ENSG00000286364 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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 = 0.241 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
ENSG00000286364	ENST00000661640.1	n.336-4072C>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.198 AC: 30161 AN: 152066 Hom.: 3357 Cov.: 33

Gnomad AFR AF: 0.190

Gnomad AMI AF: 0.258

Gnomad AMR AF: 0.133

Gnomad ASJ AF: 0.203

Gnomad EAS AF: 0.0197

Gnomad SAS AF: 0.0482

Gnomad FIN AF: 0.186

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.244

Gnomad OTH AF: 0.175

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

GnomAD4 genome AF: 0.198 AC: 30167 AN: 152184 Hom.: 3355 Cov.: 33 AF XY: 0.190 AC XY: 14121 AN XY: 74412

Gnomad4 AFR AF: 0.190

Gnomad4 AMR AF: 0.133

Gnomad4 ASJ AF: 0.203

Gnomad4 EAS AF: 0.0197

Gnomad4 SAS AF: 0.0487

Gnomad4 FIN AF: 0.186

Gnomad4 NFE AF: 0.244

Gnomad4 OTH AF: 0.175

Alfa AF: 0.148 Hom.: 343

Bravo AF: 0.197

Asia WGS AF: 0.0660 AC: 231 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	4.2
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12202284; hg19: chr6-471136;