6-31291802-C-T

Variant names:

• chr6-31291802-C-T
• rs2524163
• ENST00000755297.1:n.32+20696C>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+20696C>T 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 151,988 control chromosomes in the GnomAD database, including 33,175 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 (33175 hom., cov: 31)
• Consequence: ENSG00000298396 ENST00000755297.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.56
• Publications: 31 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 = 0.728 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000755297.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000298396	ENST00000755297.1		n.32+20696C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.657 AC: 99824 AN: 151870 Hom.: 33134 Cov.: 31

Gnomad AFR AF: 0.735

Gnomad AMI AF: 0.483

Gnomad AMR AF: 0.718

Gnomad ASJ AF: 0.581

Gnomad EAS AF: 0.720

Gnomad SAS AF: 0.688

Gnomad FIN AF: 0.669

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.594

Gnomad OTH AF: 0.682

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

GnomAD4 genome AF: 0.657 AC: 99918 AN: 151988 Hom.: 33175 Cov.: 31 AF XY: 0.662 AC XY: 49192 AN XY: 74294

African (AFR) AF: 0.735 AC: 30421 AN: 41416

American (AMR) AF: 0.718 AC: 10971 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.581 AC: 2016 AN: 3468

East Asian (EAS) AF: 0.721 AC: 3725 AN: 5168

South Asian (SAS) AF: 0.688 AC: 3312 AN: 4814

European-Finnish (FIN) AF: 0.669 AC: 7060 AN: 10560

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

European-Non Finnish (NFE) AF: 0.594 AC: 40344 AN: 67968

Other (OTH) AF: 0.682 AC: 1438 AN: 2110

Alfa AF: 0.617 Hom.: 89291

Bravo AF: 0.666

Asia WGS AF: 0.714 AC: 2482 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.6
DANN	Benign	0.16
PhyloP100		-1.6

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2524163;

hg19: chr6-31259579;