rs12449782

Variant names:

• chr17-63498888-G-A
• rs12449782
• ENST00000577647.2:n.1969+1903G>A

Your query was ambiguous. Multiple possible variants found:

• chr17-63498888-G-A
• chr17-63498888-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000577647.2(ENSG00000264813):​n.1969+1903G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.419 in 151,816 control chromosomes in the GnomAD database, including 14,284 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 0.42 (14284 hom., cov: 31)
• Consequence: ENSG00000264813 ENST00000577647.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.314

Genes affected

ENSG00000264813 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.604 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
ENSG00000264813	ENST00000577647.2	n.1969+1903G>A		intron_variant	Intron 13 of 30	2		ENSP00000464149.1

Frequencies

GnomAD3 genomes AF: 0.419 AC: 63626 AN: 151702 Hom.: 14258 Cov.: 31

Gnomad AFR AF: 0.261

Gnomad AMI AF: 0.412

Gnomad AMR AF: 0.516

Gnomad ASJ AF: 0.344

Gnomad EAS AF: 0.621

Gnomad SAS AF: 0.564

Gnomad FIN AF: 0.438

Gnomad MID AF: 0.331

Gnomad NFE AF: 0.471

Gnomad OTH AF: 0.393

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

GnomAD4 genome AF: 0.419 AC: 63685 AN: 151816 Hom.: 14284 Cov.: 31 AF XY: 0.423 AC XY: 31369 AN XY: 74176

Gnomad4 AFR AF: 0.261

Gnomad4 AMR AF: 0.517

Gnomad4 ASJ AF: 0.344

Gnomad4 EAS AF: 0.622

Gnomad4 SAS AF: 0.565

Gnomad4 FIN AF: 0.438

Gnomad4 NFE AF: 0.471

Gnomad4 OTH AF: 0.399

Alfa AF: 0.431 Hom.: 3280

Bravo AF: 0.413

Asia WGS AF: 0.626 AC: 2173 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	11
DANN	Benign	0.79

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs12449782; hg19: chr17-61576249;