chr6-31293499-A-G

Variant names:

• chr6-31293499-A-G
• rs2243868
• ENST00000755297.1:n.32+22393A>G

Variant summary

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

The ENST00000755297.1(ENSG00000298396):​n.32+22393A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.657 in 152,028 control chromosomes in the GnomAD database, including 33,177 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 0.66 (33177 hom., cov: 32)
• Consequence: ENSG00000298396 ENST00000755297.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.927
• Publications: 38 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=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.727 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+22393A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.657 AC: 99842 AN: 151912 Hom.: 33137 Cov.: 32

Gnomad AFR AF: 0.734

Gnomad AMI AF: 0.479

Gnomad AMR AF: 0.717

Gnomad ASJ AF: 0.581

Gnomad EAS AF: 0.721

Gnomad SAS AF: 0.688

Gnomad FIN AF: 0.669

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.594

Gnomad OTH AF: 0.680

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

GnomAD4 genome AF: 0.657 AC: 99934 AN: 152028 Hom.: 33177 Cov.: 32 AF XY: 0.662 AC XY: 49183 AN XY: 74302

African (AFR) AF: 0.734 AC: 30440 AN: 41460

American (AMR) AF: 0.718 AC: 10964 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.581 AC: 2014 AN: 3468

East Asian (EAS) AF: 0.722 AC: 3732 AN: 5170

South Asian (SAS) AF: 0.688 AC: 3325 AN: 4832

European-Finnish (FIN) AF: 0.669 AC: 7061 AN: 10554

Middle Eastern (MID) AF: 0.656 AC: 193 AN: 294

European-Non Finnish (NFE) AF: 0.594 AC: 40337 AN: 67954

Other (OTH) AF: 0.680 AC: 1432 AN: 2106

Alfa AF: 0.614 Hom.: 112836

Bravo AF: 0.665

Asia WGS AF: 0.714 AC: 2482 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.6
DANN	Benign	0.74
PhyloP100		-0.93

Splicing

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

Other links and lift over

dbSNP: rs2243868; hg19: chr6-31261276;