rs730570

chr14-100676553-G-A

Variant summary

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

The ENST00000557546.1(ENSG00000258717):n.104-5C>T variant causes a splice region, splice polypyrimidine tract, intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.647 in 152,896 control chromosomes in the GnomAD database, including 36,782 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 0.65 (36520 hom., cov: 31)
  • Exomes 𝑓: 0.73 (262 hom.)
• Consequence: ENST00000557546.1 splice_region, splice_polypyrimidine_tract, intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.37

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.857 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
	ENST00000557546.1	n.104-5C>T		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.647 AC: 98248 AN: 151876 Hom.: 36527 Cov.: 31

Gnomad AFR AF: 0.329

Gnomad AMI AF: 0.868

Gnomad AMR AF: 0.550

Gnomad ASJ AF: 0.852

Gnomad EAS AF: 0.212

Gnomad SAS AF: 0.587

Gnomad FIN AF: 0.776

Gnomad MID AF: 0.867

Gnomad NFE AF: 0.863

Gnomad OTH AF: 0.687

GnomAD4 exome AF: 0.733 AC: 661 AN: 902 Hom.: 262 Cov.: 0 AF XY: 0.732 AC XY: 376 AN XY: 514

Gnomad4 AFR exome AF: 0.300

Gnomad4 AMR exome AF: 0.700

Gnomad4 ASJ exome AF: 0.813

Gnomad4 EAS exome AF: 0.127

Gnomad4 SAS exome AF: 0.583

Gnomad4 FIN exome AF: 0.745

Gnomad4 NFE exome AF: 0.854

Gnomad4 OTH exome AF: 0.688

GnomAD4 genome AF: 0.646 AC: 98246 AN: 151994 Hom.: 36520 Cov.: 31 AF XY: 0.636 AC XY: 47251 AN XY: 74284

Gnomad4 AFR AF: 0.329

Gnomad4 AMR AF: 0.549

Gnomad4 ASJ AF: 0.852

Gnomad4 EAS AF: 0.211

Gnomad4 SAS AF: 0.588

Gnomad4 FIN AF: 0.776

Gnomad4 NFE AF: 0.863

Gnomad4 OTH AF: 0.679

Alfa AF: 0.824 Hom.: 81139

Bravo AF: 0.614

Asia WGS AF: 0.350 AC: 1220 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	2.2
Dann	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs730570; hg19: chr14-101142890;