rs2227319

Variant names:

• chr17-40014592-G-A
• rs2227319
• ENST00000583462.1:n.38C>T

Your query was ambiguous. Multiple possible variants found:

• chr17-40014592-G-A
• chr17-40014592-G-C

Variant summary

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

The ENST00000583462.1(ENSG00000265799):​n.38C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.308 in 152,100 control chromosomes in the GnomAD database, including 8,405 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 0.31 (8400 hom., cov: 31)
  • Exomes 𝑓: 0.35 (5 hom.)
• Consequence: ENSG00000265799 ENST00000583462.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.129

Genes affected

ENSG00000265799 (HGNC:58140):

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 (SAS) allele frequency at 95% confidence interval = 0.447 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
ENSG00000265799	ENST00000583462.1	n.38C>T		non_coding_transcript_exon_variant	Exon 1 of 2	3
ENSG00000265799	ENST00000584649.1	n.114C>T		non_coding_transcript_exon_variant	Exon 1 of 3	4

Frequencies

GnomAD3 genomes AF: 0.308 AC: 46763 AN: 151870 Hom.: 8409 Cov.: 31

Gnomad AFR AF: 0.115

Gnomad AMI AF: 0.326

Gnomad AMR AF: 0.400

Gnomad ASJ AF: 0.417

Gnomad EAS AF: 0.415

Gnomad SAS AF: 0.464

Gnomad FIN AF: 0.321

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.375

Gnomad OTH AF: 0.367

GnomAD4 exome AF: 0.348 AC: 39 AN: 112 Hom.: 5 Cov.: 0 AF XY: 0.351 AC XY: 26 AN XY: 74

Gnomad4 AFR exome AF: 0.500

Gnomad4 EAS exome AF: 0.333

Gnomad4 FIN exome AF: 0.200

Gnomad4 NFE exome AF: 0.371

Gnomad4 OTH exome AF: 0.429

GnomAD4 genome AF: 0.308 AC: 46751 AN: 151988 Hom.: 8400 Cov.: 31 AF XY: 0.309 AC XY: 22933 AN XY: 74272

Gnomad4 AFR AF: 0.115

Gnomad4 AMR AF: 0.399

Gnomad4 ASJ AF: 0.417

Gnomad4 EAS AF: 0.415

Gnomad4 SAS AF: 0.463

Gnomad4 FIN AF: 0.321

Gnomad4 NFE AF: 0.375

Gnomad4 OTH AF: 0.365

Alfa AF: 0.325 Hom.: 2939

Bravo AF: 0.308

Asia WGS AF: 0.406 AC: 1417 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	3.3
DANN	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2227319; hg19: chr17-38170845;