rs12213468

Variant names:

• chr6-156336708-G-A
• rs12213468
• ENST00000663591.1:n.225-41954C>T

Variant summary

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

The ENST00000663591.1(ENSG00000287092):​n.225-41954C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.235 in 152,174 control chromosomes in the GnomAD database, including 4,869 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 0.24 (4869 hom., cov: 32)
• Consequence: ENSG00000287092 ENST00000663591.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0550
• Publications: 2 publications found

Genes affected

ENSG00000287092 (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 = 0.303 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105378071	XR_943136.3	n.130-13813G>A		intron_variant	Intron 1 of 5
LOC105378071	XR_943139.3	n.221-13813G>A		intron_variant	Intron 2 of 6
LOC105378071	XR_943140.3	n.221-13813G>A		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000287092	ENST00000663591.1	n.225-41954C>T		intron_variant	Intron 1 of 3
ENSG00000287092	ENST00000789128.1	n.200-5687C>T		intron_variant	Intron 1 of 3
ENSG00000287092	ENST00000789132.1	n.216-5687C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.235 AC: 35770 AN: 152056 Hom.: 4873 Cov.: 32

Gnomad AFR AF: 0.108

Gnomad AMI AF: 0.235

Gnomad AMR AF: 0.221

Gnomad ASJ AF: 0.269

Gnomad EAS AF: 0.0993

Gnomad SAS AF: 0.256

Gnomad FIN AF: 0.339

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.306

Gnomad OTH AF: 0.253

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

GnomAD4 genome AF: 0.235 AC: 35767 AN: 152174 Hom.: 4869 Cov.: 32 AF XY: 0.236 AC XY: 17537 AN XY: 74404

African (AFR) AF: 0.108 AC: 4485 AN: 41528

American (AMR) AF: 0.221 AC: 3382 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.269 AC: 935 AN: 3470

East Asian (EAS) AF: 0.0998 AC: 517 AN: 5182

South Asian (SAS) AF: 0.257 AC: 1239 AN: 4822

European-Finnish (FIN) AF: 0.339 AC: 3583 AN: 10568

Middle Eastern (MID) AF: 0.252 AC: 74 AN: 294

European-Non Finnish (NFE) AF: 0.306 AC: 20809 AN: 67990

Other (OTH) AF: 0.250 AC: 529 AN: 2112

Alfa AF: 0.269 Hom.: 12822

Bravo AF: 0.220

Asia WGS AF: 0.144 AC: 508 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	0.94
DANN	Benign	0.25
PhyloP100		0.055

Splicing

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

Other links and lift over

dbSNP: rs12213468; hg19: chr6-156657842;