rs954353

Variant names:

• chr1-85578968-A-G
• rs954353
• ENST00000609367.1:n.-226T>C

Your query was ambiguous. Multiple possible variants found:

• chr1-85578968-A-G
• chr1-85578968-A-T

Variant summary

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

The ENST00000609367.1(ENSG00000272691):​n.-226T>C variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.411 in 151,730 control chromosomes in the GnomAD database, including 13,028 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 0.41 (13028 hom., cov: 30)
• Consequence: ENSG00000272691 ENST00000609367.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.24

Genes affected

ENSG00000272691 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.436 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
ENSG00000272691	ENST00000609367.1	n.-226T>C		upstream_gene_variant		6

Frequencies

GnomAD3 genomes AF: 0.411 AC: 62345 AN: 151608 Hom.: 13030 Cov.: 30

Gnomad AFR AF: 0.407

Gnomad AMI AF: 0.391

Gnomad AMR AF: 0.324

Gnomad ASJ AF: 0.423

Gnomad EAS AF: 0.390

Gnomad SAS AF: 0.249

Gnomad FIN AF: 0.456

Gnomad MID AF: 0.348

Gnomad NFE AF: 0.440

Gnomad OTH AF: 0.383

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

GnomAD4 genome AF: 0.411 AC: 62364 AN: 151730 Hom.: 13028 Cov.: 30 AF XY: 0.405 AC XY: 29999 AN XY: 74118

Gnomad4 AFR AF: 0.406

Gnomad4 AMR AF: 0.324

Gnomad4 ASJ AF: 0.423

Gnomad4 EAS AF: 0.391

Gnomad4 SAS AF: 0.249

Gnomad4 FIN AF: 0.456

Gnomad4 NFE AF: 0.440

Gnomad4 OTH AF: 0.381

Alfa AF: 0.370 Hom.: 2079

Bravo AF: 0.401

Asia WGS AF: 0.359 AC: 1251 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	14
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs954353; hg19: chr1-86044651;