rs17348299

Variant names:

• chr5-56027067-C-A
• rs17348299
• ENST00000645512.1:n.279+32866C>A

Your query was ambiguous. Multiple possible variants found:

• chr5-56027067-C-A
• chr5-56027067-C-T

Variant summary

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

The ENST00000645512.1(ENSG00000249236):​n.279+32866C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.117 in 152,198 control chromosomes in the GnomAD database, including 1,245 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 0.12 (1245 hom., cov: 32)
• Consequence: ENSG00000249236 ENST00000645512.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0780

Genes affected

ENSG00000249236 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.62).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.199 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
ENSG00000249236	ENST00000645512.1	n.279+32866C>A		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.117 AC: 17792 AN: 152080 Hom.: 1247 Cov.: 32

Gnomad AFR AF: 0.0542

Gnomad AMI AF: 0.163

Gnomad AMR AF: 0.106

Gnomad ASJ AF: 0.171

Gnomad EAS AF: 0.0568

Gnomad SAS AF: 0.210

Gnomad FIN AF: 0.113

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.152

Gnomad OTH AF: 0.133

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

GnomAD4 genome AF: 0.117 AC: 17787 AN: 152198 Hom.: 1245 Cov.: 32 AF XY: 0.115 AC XY: 8559 AN XY: 74410

African (AFR) AF: 0.0541 AC: 2246 AN: 41546

American (AMR) AF: 0.105 AC: 1613 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.171 AC: 593 AN: 3470

East Asian (EAS) AF: 0.0567 AC: 294 AN: 5186

South Asian (SAS) AF: 0.210 AC: 1013 AN: 4828

European-Finnish (FIN) AF: 0.113 AC: 1196 AN: 10576

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.152 AC: 10353 AN: 67984

Other (OTH) AF: 0.135 AC: 285 AN: 2112

Alfa AF: 0.136 Hom.: 4826

Bravo AF: 0.110

Asia WGS AF: 0.127 AC: 442 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.62
CADD	Benign	4.7
DANN	Benign	0.64
PhyloP100		0.078

Splicing

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

Publications

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Other links and lift over

dbSNP: rs17348299; hg19: chr5-55322895;