1-55862923-G-T

Variant names:

• chr1-55862923-G-T
• rs4926698
• ENST00000424357.1:n.367-9G>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 intron 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: ENSG00000234810 ENST00000424357.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.487

Genes affected

ENSG00000234810 (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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000234810	ENST00000424357.1	n.367-9G>T		intron_variant	Intron 3 of 4	3
ENSG00000234810	ENST00000646266.1	n.357+15386G>T		intron_variant	Intron 3 of 11
ENSG00000234810	ENST00000659410.1	n.376+15386G>T		intron_variant	Intron 3 of 3

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;