rs2571343

Variant names:

• chr12-93941104-C-A
• rs2571343
• ENST00000550687.1:n.59+2441G>T

Your query was ambiguous. Multiple possible variants found:

• chr12-93941104-C-A
• chr12-93941104-C-G
• chr12-93941104-C-T

Variant summary

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

The ENST00000550687.1(ENSG00000257283):​n.59+2441G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.127 in 152,024 control chromosomes in the GnomAD database, including 1,583 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 0.13 (1583 hom., cov: 31)
• Consequence: ENSG00000257283 ENST00000550687.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.322
• Publications: 1 publications found

Genes affected

ENSG00000257283 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.408 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000550687.1. 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
	LOC105369911	NR_135017.1		n.62+2441G>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000257283	ENST00000550687.1	TSL:4	n.59+2441G>T		intron	N/A
	ENSG00000257283	ENST00000786429.1		n.197-32099G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.127 AC: 19328 AN: 151906 Hom.: 1570 Cov.: 31

Gnomad AFR AF: 0.0952

Gnomad AMI AF: 0.112

Gnomad AMR AF: 0.180

Gnomad ASJ AF: 0.0954

Gnomad EAS AF: 0.423

Gnomad SAS AF: 0.253

Gnomad FIN AF: 0.152

Gnomad MID AF: 0.0924

Gnomad NFE AF: 0.101

Gnomad OTH AF: 0.143

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

GnomAD4 genome AF: 0.127 AC: 19362 AN: 152024 Hom.: 1583 Cov.: 31 AF XY: 0.135 AC XY: 10021 AN XY: 74286

African (AFR) AF: 0.0951 AC: 3946 AN: 41488

American (AMR) AF: 0.181 AC: 2760 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.0954 AC: 331 AN: 3470

East Asian (EAS) AF: 0.423 AC: 2174 AN: 5142

South Asian (SAS) AF: 0.253 AC: 1214 AN: 4800

European-Finnish (FIN) AF: 0.152 AC: 1609 AN: 10584

Middle Eastern (MID) AF: 0.0856 AC: 25 AN: 292

European-Non Finnish (NFE) AF: 0.101 AC: 6878 AN: 67962

Other (OTH) AF: 0.153 AC: 323 AN: 2108

Alfa AF: 0.110 Hom.: 3106

Bravo AF: 0.129

Asia WGS AF: 0.366 AC: 1271 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.2
DANN	Benign	0.70
PhyloP100		-0.32

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: rs2571343;

hg19: chr12-94334880;