1-151833835-A-T

Variant names:

• chr1-151833835-A-T
• rs4284267
• ENST00000796615.1:n.562A>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000796615.1(ENSG00000303697):​n.562A>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.942 in 152,234 control chromosomes in the GnomAD database, including 67,703 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 0.94 (67703 hom., cov: 32)
• Consequence: ENSG00000303697 ENST00000796615.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.845
• Publications: 5 publications found

Genes affected

ENSG00000303697 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 = 0.969 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
ENSG00000303697	ENST00000796615.1	n.562A>T		non_coding_transcript_exon_variant	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.943 AC: 143379 AN: 152116 Hom.: 67662 Cov.: 32

Gnomad AFR AF: 0.897

Gnomad AMI AF: 0.831

Gnomad AMR AF: 0.962

Gnomad ASJ AF: 0.973

Gnomad EAS AF: 0.992

Gnomad SAS AF: 0.957

Gnomad FIN AF: 0.979

Gnomad MID AF: 0.959

Gnomad NFE AF: 0.955

Gnomad OTH AF: 0.945

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

GnomAD4 genome AF: 0.942 AC: 143476 AN: 152234 Hom.: 67703 Cov.: 32 AF XY: 0.945 AC XY: 70340 AN XY: 74432

African (AFR) AF: 0.897 AC: 37240 AN: 41522

American (AMR) AF: 0.962 AC: 14709 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.973 AC: 3376 AN: 3468

East Asian (EAS) AF: 0.991 AC: 5128 AN: 5172

South Asian (SAS) AF: 0.957 AC: 4615 AN: 4822

European-Finnish (FIN) AF: 0.979 AC: 10401 AN: 10620

Middle Eastern (MID) AF: 0.956 AC: 281 AN: 294

European-Non Finnish (NFE) AF: 0.955 AC: 64975 AN: 68020

Other (OTH) AF: 0.945 AC: 1993 AN: 2108

Alfa AF: 0.948 Hom.: 8487

Bravo AF: 0.940

Asia WGS AF: 0.974 AC: 3387 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	0.87
DANN	Benign	0.57
PhyloP100		-0.84

Splicing

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

Other links and lift over

dbSNP: rs4284267; hg19: chr1-151806311;