rs12176541

Variant names:

• chr6-48562562-G-A
• rs12176541
• ENST00000730502.1:n.282+23281G>A

Your query was ambiguous. Multiple possible variants found:

• chr6-48562562-G-A
• chr6-48562562-G-T

Variant summary

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

The ENST00000730502.1(ENSG00000295504):​n.282+23281G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0847 in 152,144 control chromosomes in the GnomAD database, including 1,610 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 0.085 (1610 hom., cov: 32)
• Consequence: ENSG00000295504 ENST00000730502.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.273
• Publications: 3 publications found

Genes affected

ENSG00000295504 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.486 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000730502.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000295504	ENST00000730502.1		n.282+23281G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0846 AC: 12856 AN: 152026 Hom.: 1592 Cov.: 32

Gnomad AFR AF: 0.0159

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.268

Gnomad ASJ AF: 0.0403

Gnomad EAS AF: 0.503

Gnomad SAS AF: 0.169

Gnomad FIN AF: 0.0594

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0550

Gnomad OTH AF: 0.0866

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

GnomAD4 genome AF: 0.0847 AC: 12889 AN: 152144 Hom.: 1610 Cov.: 32 AF XY: 0.0908 AC XY: 6756 AN XY: 74374

African (AFR) AF: 0.0158 AC: 658 AN: 41534

American (AMR) AF: 0.269 AC: 4113 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.0403 AC: 140 AN: 3470

East Asian (EAS) AF: 0.503 AC: 2591 AN: 5156

South Asian (SAS) AF: 0.169 AC: 814 AN: 4820

European-Finnish (FIN) AF: 0.0594 AC: 629 AN: 10594

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.0550 AC: 3736 AN: 67980

Other (OTH) AF: 0.0933 AC: 197 AN: 2112

Alfa AF: 0.0690 Hom.: 2650

Bravo AF: 0.102

Asia WGS AF: 0.308 AC: 1068 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.8
DANN	Benign	0.70
PhyloP100		0.27

Splicing

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

Other links and lift over

dbSNP: rs12176541; hg19: chr6-48530298;