rs12471454

Variant names:

• chr2-199149760-T-C
• rs12471454
• ENST00000827186.1:n.130+39317A>G

Your query was ambiguous. Multiple possible variants found:

• chr2-199149760-T-C
• chr2-199149760-T-G

Variant summary

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

The ENST00000827186.1(ENSG00000307577):​n.130+39317A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.529 in 138,086 control chromosomes in the GnomAD database, including 19,085 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 0.53 (19085 hom., cov: 28)
• Consequence: ENSG00000307577 ENST00000827186.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.437
• Publications: 3 publications found

Genes affected

ENSG00000307577 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.593 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000307577	ENST00000827186.1	n.130+39317A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.529 AC: 72979 AN: 137994 Hom.: 19092 Cov.: 28

Gnomad AFR AF: 0.385

Gnomad AMI AF: 0.557

Gnomad AMR AF: 0.538

Gnomad ASJ AF: 0.561

Gnomad EAS AF: 0.335

Gnomad SAS AF: 0.491

Gnomad FIN AF: 0.668

Gnomad MID AF: 0.536

Gnomad NFE AF: 0.598

Gnomad OTH AF: 0.523

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

GnomAD4 genome AF: 0.529 AC: 72983 AN: 138086 Hom.: 19085 Cov.: 28 AF XY: 0.530 AC XY: 35710 AN XY: 67332

African (AFR) AF: 0.384 AC: 13583 AN: 35352

American (AMR) AF: 0.538 AC: 7517 AN: 13970

Ashkenazi Jewish (ASJ) AF: 0.561 AC: 1817 AN: 3240

East Asian (EAS) AF: 0.334 AC: 1435 AN: 4292

South Asian (SAS) AF: 0.491 AC: 2070 AN: 4214

European-Finnish (FIN) AF: 0.668 AC: 6532 AN: 9778

Middle Eastern (MID) AF: 0.534 AC: 142 AN: 266

European-Non Finnish (NFE) AF: 0.598 AC: 38416 AN: 64210

Other (OTH) AF: 0.521 AC: 1000 AN: 1918

Alfa AF: 0.548 Hom.: 15940

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.4
DANN	Benign	0.75
PhyloP100		-0.44

Splicing

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

Other links and lift over

dbSNP: rs12471454; hg19: chr2-200014483;