rs12208888

Variant names:

• chr6-31279653-C-T
• rs12208888
• ENST00000755297.1:n.32+8547C>T

Variant summary

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

The ENST00000755297.1(ENSG00000298396):​n.32+8547C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.126 in 152,210 control chromosomes in the GnomAD database, including 1,327 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 0.13 (1327 hom., cov: 32)
• Consequence: ENSG00000298396 ENST00000755297.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.870
• Publications: 6 publications found

Genes affected

ENSG00000298396 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.169 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
ENSG00000298396	ENST00000755297.1	n.32+8547C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.126 AC: 19192 AN: 152092 Hom.: 1327 Cov.: 32

Gnomad AFR AF: 0.106

Gnomad AMI AF: 0.221

Gnomad AMR AF: 0.111

Gnomad ASJ AF: 0.309

Gnomad EAS AF: 0.0670

Gnomad SAS AF: 0.180

Gnomad FIN AF: 0.100

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.135

Gnomad OTH AF: 0.140

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

GnomAD4 genome AF: 0.126 AC: 19200 AN: 152210 Hom.: 1327 Cov.: 32 AF XY: 0.127 AC XY: 9429 AN XY: 74408

African (AFR) AF: 0.106 AC: 4403 AN: 41524

American (AMR) AF: 0.110 AC: 1686 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.309 AC: 1070 AN: 3466

East Asian (EAS) AF: 0.0673 AC: 349 AN: 5184

South Asian (SAS) AF: 0.178 AC: 860 AN: 4820

European-Finnish (FIN) AF: 0.100 AC: 1060 AN: 10596

Middle Eastern (MID) AF: 0.235 AC: 69 AN: 294

European-Non Finnish (NFE) AF: 0.135 AC: 9206 AN: 68008

Other (OTH) AF: 0.140 AC: 296 AN: 2116

Alfa AF: 0.133 Hom.: 198

Bravo AF: 0.125

Asia WGS AF: 0.133 AC: 463 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.3
DANN	Benign	0.53
PhyloP100		-0.87

Splicing

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

Other links and lift over

dbSNP: rs12208888; hg19: chr6-31247430;