rs2227319

Positions:

• 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: ENST00000583462.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.129

Genes affected

(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 (SAS) allele frequency at 95% confidence interval = 0.447 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000583462.1	n.38C>T		non_coding_transcript_exon_variant	1/2	3
	ENST00000584649.1	n.114C>T		non_coding_transcript_exon_variant	1/3	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;