rs854273

Variant names:

• chr1-68777791-A-C
• rs854273
• ENST00000643361.1:n.418+79341A>C

Your query was ambiguous. Multiple possible variants found:

• chr1-68777791-A-C
• chr1-68777791-A-G
• chr1-68777791-A-T

Variant summary

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

The ENST00000643361.1(ENSG00000285407):​n.418+79341A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.799 in 152,048 control chromosomes in the GnomAD database, including 48,710 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 0.80 (48710 hom., cov: 32)
• Consequence: ENSG00000285407 ENST00000643361.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.567

Genes affected

ENSG00000285407 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.826 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+79341A>C		intron_variant	Intron 2 of 6

Frequencies

GnomAD3 genomes AF: 0.799 AC: 121419 AN: 151930 Hom.: 48676 Cov.: 32

Gnomad AFR AF: 0.764

Gnomad AMI AF: 0.821

Gnomad AMR AF: 0.771

Gnomad ASJ AF: 0.767

Gnomad EAS AF: 0.847

Gnomad SAS AF: 0.816

Gnomad FIN AF: 0.810

Gnomad MID AF: 0.826

Gnomad NFE AF: 0.822

Gnomad OTH AF: 0.792

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

GnomAD4 genome AF: 0.799 AC: 121510 AN: 152048 Hom.: 48710 Cov.: 32 AF XY: 0.802 AC XY: 59579 AN XY: 74334

Gnomad4 AFR AF: 0.764

Gnomad4 AMR AF: 0.771

Gnomad4 ASJ AF: 0.767

Gnomad4 EAS AF: 0.847

Gnomad4 SAS AF: 0.816

Gnomad4 FIN AF: 0.810

Gnomad4 NFE AF: 0.822

Gnomad4 OTH AF: 0.794

Alfa AF: 0.821 Hom.: 101279

Bravo AF: 0.792

Asia WGS AF: 0.837 AC: 2910 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.79
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs854273; hg19: chr1-69243474;