rs2524057

Variant names:

• chr6-31284118-A-G
• rs2524057
• ENST00000755297.1:n.32+13012A>G

Your query was ambiguous. Multiple possible variants found:

• chr6-31284118-A-G
• chr6-31284118-A-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+13012A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.156 in 152,286 control chromosomes in the GnomAD database, including 2,054 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 0.16 (2054 hom., cov: 33)
• Consequence: ENSG00000298396 ENST00000755297.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.52
• Publications: 11 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=-1.01).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.229 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+13012A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.156 AC: 23685 AN: 152168 Hom.: 2053 Cov.: 33

Gnomad AFR AF: 0.106

Gnomad AMI AF: 0.154

Gnomad AMR AF: 0.235

Gnomad ASJ AF: 0.183

Gnomad EAS AF: 0.181

Gnomad SAS AF: 0.195

Gnomad FIN AF: 0.118

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.168

Gnomad OTH AF: 0.165

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

GnomAD4 genome AF: 0.156 AC: 23689 AN: 152286 Hom.: 2054 Cov.: 33 AF XY: 0.154 AC XY: 11472 AN XY: 74474

African (AFR) AF: 0.106 AC: 4402 AN: 41570

American (AMR) AF: 0.236 AC: 3609 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.183 AC: 634 AN: 3470

East Asian (EAS) AF: 0.181 AC: 938 AN: 5174

South Asian (SAS) AF: 0.194 AC: 936 AN: 4828

European-Finnish (FIN) AF: 0.118 AC: 1248 AN: 10612

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.168 AC: 11397 AN: 68004

Other (OTH) AF: 0.164 AC: 347 AN: 2114

Alfa AF: 0.123 Hom.: 593

Bravo AF: 0.163

Asia WGS AF: 0.226 AC: 785 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	5.1
DANN	Benign	0.26
PhyloP100		-3.5

Splicing

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

Other links and lift over

dbSNP: rs2524057; hg19: chr6-31251895;