1-68747332-C-T

Variant names:

• chr1-68747332-C-T
• rs1388654
• ENST00000643361.1:n.418+48882C>T

Variant summary

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

The ENST00000643361.1(ENSG00000285407):​n.418+48882C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.705 in 152,102 control chromosomes in the GnomAD database, including 38,883 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 0.70 (38883 hom., cov: 33)
• Consequence: ENSG00000285407 ENST00000643361.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.168

Genes affected

ENSG00000285407 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.825 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
ENSG00000285407	ENST00000643361.1	n.418+48882C>T		intron_variant	Intron 2 of 6

Frequencies

GnomAD3 genomes AF: 0.705 AC: 107157 AN: 151984 Hom.: 38881 Cov.: 33

Gnomad AFR AF: 0.523

Gnomad AMI AF: 0.822

Gnomad AMR AF: 0.723

Gnomad ASJ AF: 0.740

Gnomad EAS AF: 0.845

Gnomad SAS AF: 0.778

Gnomad FIN AF: 0.743

Gnomad MID AF: 0.756

Gnomad NFE AF: 0.786

Gnomad OTH AF: 0.719

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.705 AC: 107192 AN: 152102 Hom.: 38883 Cov.: 33 AF XY: 0.708 AC XY: 52623 AN XY: 74348

Gnomad4 AFR AF: 0.523

Gnomad4 AMR AF: 0.724

Gnomad4 ASJ AF: 0.740

Gnomad4 EAS AF: 0.846

Gnomad4 SAS AF: 0.778

Gnomad4 FIN AF: 0.743

Gnomad4 NFE AF: 0.786

Gnomad4 OTH AF: 0.722

Alfa AF: 0.726 Hom.: 5102

Bravo AF: 0.693

Asia WGS AF: 0.799 AC: 2779 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	7.5
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1388654; hg19: chr1-69213015;