chr6-31284619-A-C

Variant names:

• chr6-31284619-A-C
• rs2524054
• ENST00000755297.1:n.32+13513A>C

Variant summary

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

The ENST00000755297.1(ENSG00000298396):​n.32+13513A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.813 in 152,146 control chromosomes in the GnomAD database, including 50,886 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 0.81 (50886 hom., cov: 31)
• Consequence: ENSG00000298396 ENST00000755297.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.26
• Publications: 48 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=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.903 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+13513A>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.813 AC: 123637 AN: 152028 Hom.: 50830 Cov.: 31

Gnomad AFR AF: 0.910

Gnomad AMI AF: 0.707

Gnomad AMR AF: 0.851

Gnomad ASJ AF: 0.929

Gnomad EAS AF: 0.838

Gnomad SAS AF: 0.880

Gnomad FIN AF: 0.775

Gnomad MID AF: 0.934

Gnomad NFE AF: 0.739

Gnomad OTH AF: 0.857

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

GnomAD4 genome AF: 0.813 AC: 123746 AN: 152146 Hom.: 50886 Cov.: 31 AF XY: 0.819 AC XY: 60876 AN XY: 74364

African (AFR) AF: 0.911 AC: 37807 AN: 41518

American (AMR) AF: 0.851 AC: 13014 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.929 AC: 3223 AN: 3470

East Asian (EAS) AF: 0.838 AC: 4345 AN: 5182

South Asian (SAS) AF: 0.878 AC: 4234 AN: 4820

European-Finnish (FIN) AF: 0.775 AC: 8191 AN: 10572

Middle Eastern (MID) AF: 0.932 AC: 274 AN: 294

European-Non Finnish (NFE) AF: 0.739 AC: 50204 AN: 67976

Other (OTH) AF: 0.857 AC: 1809 AN: 2112

Alfa AF: 0.764 Hom.: 136318

Bravo AF: 0.823

Asia WGS AF: 0.882 AC: 3067 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.3
DANN	Benign	0.64
PhyloP100		-3.3

Splicing

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

Other links and lift over

dbSNP: rs2524054; hg19: chr6-31252396;