1-55862923-G-T

Position:

• chr1-55862923-G-T

Variant summary

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

The ENST00000424357.1(ENSG00000234810):​n.367-9G>T variant causes a 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 0.449 in 151,800 control chromosomes in the GnomAD database, including 15,702 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 0.45 (15702 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: ENST00000424357.1 splice_polypyrimidine_tract, intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.487

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.563 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000424357.1	n.367-9G>T		splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant		3
	ENST00000646266.1	n.357+15386G>T		intron_variant, non_coding_transcript_variant
	ENST00000659410.1	n.376+15386G>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.449 AC: 68110 AN: 151682 Hom.: 15686 Cov.: 32

Gnomad AFR AF: 0.396

Gnomad AMI AF: 0.398

Gnomad AMR AF: 0.572

Gnomad ASJ AF: 0.404

Gnomad EAS AF: 0.271

Gnomad SAS AF: 0.370

Gnomad FIN AF: 0.382

Gnomad MID AF: 0.312

Gnomad NFE AF: 0.487

Gnomad OTH AF: 0.448

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.449 AC: 68156 AN: 151800 Hom.: 15702 Cov.: 32 AF XY: 0.444 AC XY: 32914 AN XY: 74178

Gnomad4 AFR AF: 0.395

Gnomad4 AMR AF: 0.573

Gnomad4 ASJ AF: 0.404

Gnomad4 EAS AF: 0.271

Gnomad4 SAS AF: 0.369

Gnomad4 FIN AF: 0.382

Gnomad4 NFE AF: 0.487

Gnomad4 OTH AF: 0.442

Alfa AF: 0.485 Hom.: 4465

Bravo AF: 0.459

Asia WGS AF: 0.338 AC: 1170 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	5.6
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4926698; hg19: chr1-56328596;