rs2664588

chr20-47951890-C-T

Variant summary

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

The ENST00000659337.1(ENSG00000234967):n.163+45C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.346 in 152,166 control chromosomes in the GnomAD database, including 11,031 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 0.35 (11030 hom., cov: 32)
  • Exomes 𝑓: 0.21 (1 hom.)
• Consequence: ENST00000659337.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.07

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.443 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105372637	XR_936788.2	n.204+45C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000659337.1	n.163+45C>T		intron_variant, non_coding_transcript_variant
	ENST00000431915.1	n.260C>T		non_coding_transcript_exon_variant	2/2	2
	ENST00000666669.1	n.262C>T		non_coding_transcript_exon_variant	2/2
	ENST00000662435.1	n.196+45C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.347 AC: 52705 AN: 151942 Hom.: 11035 Cov.: 32

Gnomad AFR AF: 0.112

Gnomad AMI AF: 0.479

Gnomad AMR AF: 0.452

Gnomad ASJ AF: 0.494

Gnomad EAS AF: 0.109

Gnomad SAS AF: 0.389

Gnomad FIN AF: 0.506

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.446

Gnomad OTH AF: 0.369

GnomAD4 exome AF: 0.208 AC: 22 AN: 106 Hom.: 1 Cov.: 0 AF XY: 0.197 AC XY: 13 AN XY: 66

Gnomad4 FIN exome AF: 0.156

Gnomad4 NFE exome AF: 0.500

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.347 AC: 52699 AN: 152060 Hom.: 11030 Cov.: 32 AF XY: 0.349 AC XY: 25959 AN XY: 74324

Gnomad4 AFR AF: 0.112

Gnomad4 AMR AF: 0.452

Gnomad4 ASJ AF: 0.494

Gnomad4 EAS AF: 0.109

Gnomad4 SAS AF: 0.388

Gnomad4 FIN AF: 0.506

Gnomad4 NFE AF: 0.446

Gnomad4 OTH AF: 0.364

Alfa AF: 0.425 Hom.: 8167

Bravo AF: 0.332

Asia WGS AF: 0.225 AC: 785 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	0.55
Dann	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2664588; hg19: chr20-46580634;