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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107986602	XR_001744151.1	n.466+23281G>A		intron_variant	Intron 3 of 3
LOC107986602	XR_001744152.1	n.234+23281G>A		intron_variant	Intron 2 of 2
LOC107986602	XR_001744154.1	n.455+23281G>A		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000295504	ENST00000730502.1	n.282+23281G>A		intron_variant	Intron 2 of 2

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 v4.3

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;