1-53471504-A-G

Variant names:

• chr1-53471504-A-G
• rs1296438
• ENST00000748744.1:n.57A>G

Variant summary

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

The ENST00000748744.1(ENSG00000297533):​n.57A>G 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 0.392 in 152,056 control chromosomes in the GnomAD database, including 14,395 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 0.39 (14395 hom., cov: 33)
• Consequence: ENSG00000297533 ENST00000748744.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -5.28
• Publications: 2 publications found

Genes affected

ENSG00000297533 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.678 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000748744.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000297533	ENST00000748744.1		n.57A>G		non_coding_transcript_exon	Exon 1 of 2
	ENSG00000297533	ENST00000748745.1		n.-53A>G		upstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.391 AC: 59464 AN: 151938 Hom.: 14360 Cov.: 33

Gnomad AFR AF: 0.684

Gnomad AMI AF: 0.120

Gnomad AMR AF: 0.254

Gnomad ASJ AF: 0.271

Gnomad EAS AF: 0.518

Gnomad SAS AF: 0.392

Gnomad FIN AF: 0.241

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.269

Gnomad OTH AF: 0.364

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

GnomAD4 genome AF: 0.392 AC: 59554 AN: 152056 Hom.: 14395 Cov.: 33 AF XY: 0.388 AC XY: 28837 AN XY: 74306

African (AFR) AF: 0.684 AC: 28382 AN: 41464

American (AMR) AF: 0.253 AC: 3869 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.271 AC: 940 AN: 3466

East Asian (EAS) AF: 0.518 AC: 2667 AN: 5148

South Asian (SAS) AF: 0.392 AC: 1891 AN: 4822

European-Finnish (FIN) AF: 0.241 AC: 2550 AN: 10584

Middle Eastern (MID) AF: 0.320 AC: 94 AN: 294

European-Non Finnish (NFE) AF: 0.269 AC: 18283 AN: 67968

Other (OTH) AF: 0.364 AC: 769 AN: 2114

Alfa AF: 0.286 Hom.: 3877

Bravo AF: 0.405

Asia WGS AF: 0.462 AC: 1607 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.0030
DANN	Benign	0.47
PhyloP100		-5.3

Splicing

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

Other links and lift over

dbSNP: rs1296438; hg19: chr1-53937177;