6-31368473-A-G

Variant names:

• chr6-31368473-A-G
• rs2523535
• ENST00000649421.2:n.274+1143A>G

Variant summary

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

The ENST00000649421.2(ENSG00000285647):​n.274+1143A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.315 in 152,186 control chromosomes in the GnomAD database, including 8,066 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 0.31 (8066 hom., cov: 33)
• Consequence: ENSG00000285647 ENST00000649421.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.660
• Publications: 35 publications found

Genes affected

ENSG00000285647 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.384 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000649421.2. 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
	ENSG00000285647	ENST00000649421.2		n.274+1143A>G		intron	N/A
	ENSG00000298426	ENST00000755446.1		n.327-13507A>G		intron	N/A
	ENSG00000285647	ENST00000755530.1		n.203-6410A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.315 AC: 47890 AN: 152068 Hom.: 8063 Cov.: 33

Gnomad AFR AF: 0.258

Gnomad AMI AF: 0.375

Gnomad AMR AF: 0.265

Gnomad ASJ AF: 0.177

Gnomad EAS AF: 0.214

Gnomad SAS AF: 0.225

Gnomad FIN AF: 0.272

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.388

Gnomad OTH AF: 0.316

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

GnomAD4 genome AF: 0.315 AC: 47911 AN: 152186 Hom.: 8066 Cov.: 33 AF XY: 0.304 AC XY: 22597 AN XY: 74384

African (AFR) AF: 0.258 AC: 10719 AN: 41500

American (AMR) AF: 0.265 AC: 4044 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.177 AC: 613 AN: 3470

East Asian (EAS) AF: 0.213 AC: 1104 AN: 5184

South Asian (SAS) AF: 0.225 AC: 1088 AN: 4826

European-Finnish (FIN) AF: 0.272 AC: 2885 AN: 10602

Middle Eastern (MID) AF: 0.293 AC: 86 AN: 294

European-Non Finnish (NFE) AF: 0.388 AC: 26368 AN: 67998

Other (OTH) AF: 0.313 AC: 662 AN: 2112

Alfa AF: 0.356 Hom.: 28503

Bravo AF: 0.314

Asia WGS AF: 0.231 AC: 803 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	6.2
DANN	Benign	0.43
PhyloP100		-0.66

Splicing

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

Other links and lift over

dbSNP: rs2523535; hg19: chr6-31336250;