chr6-31333042-T-C

Variant names:

• chr6-31333042-T-C
• rs12212594
• ENST00000755297.1:n.33-23159T>C

Variant summary

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

The ENST00000755297.1(ENSG00000298396):​n.33-23159T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0541 in 152,308 control chromosomes in the GnomAD database, including 288 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 0.054 (288 hom., cov: 32)
• Consequence: ENSG00000298396 ENST00000755297.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0770
• Publications: 16 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=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.079 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.33-23159T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0542 AC: 8248 AN: 152190 Hom.: 289 Cov.: 32

Gnomad AFR AF: 0.0159

Gnomad AMI AF: 0.190

Gnomad AMR AF: 0.0333

Gnomad ASJ AF: 0.0757

Gnomad EAS AF: 0.0383

Gnomad SAS AF: 0.0866

Gnomad FIN AF: 0.0593

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0775

Gnomad OTH AF: 0.0493

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

GnomAD4 genome AF: 0.0541 AC: 8245 AN: 152308 Hom.: 288 Cov.: 32 AF XY: 0.0546 AC XY: 4068 AN XY: 74478

African (AFR) AF: 0.0160 AC: 665 AN: 41582

American (AMR) AF: 0.0332 AC: 508 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0757 AC: 263 AN: 3472

East Asian (EAS) AF: 0.0384 AC: 199 AN: 5188

South Asian (SAS) AF: 0.0858 AC: 414 AN: 4824

European-Finnish (FIN) AF: 0.0593 AC: 629 AN: 10608

Middle Eastern (MID) AF: 0.0680 AC: 20 AN: 294

European-Non Finnish (NFE) AF: 0.0775 AC: 5272 AN: 68022

Other (OTH) AF: 0.0483 AC: 102 AN: 2110

Alfa AF: 0.0598 Hom.: 85

Bravo AF: 0.0507

Asia WGS AF: 0.0520 AC: 182 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	9.9
DANN	Benign	0.50
PhyloP100		0.077

Splicing

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

Other links and lift over

dbSNP: rs12212594; hg19: chr6-31300819;