chr1-53418785-C-T

Variant names:

• chr1-53418785-C-T
• rs1776421
• ENST00000566461.2:c.*57-1119G>A

Variant summary

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

The ENST00000566461.2(ENSG00000293253):​c.*57-1119G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.228 in 151,682 control chromosomes in the GnomAD database, including 4,817 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 0.23 (4817 hom., cov: 31)
• Consequence: ENSG00000293253 ENST00000566461.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.97
• Publications: 3 publications found

Genes affected

ENSG00000293253 (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 = 0.392 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
ENSG00000293253	ENST00000566461.2	c.*57-1119G>A		intron_variant	Intron 1 of 3	3		ENSP00000520458.1
ENSG00000293253	ENST00000715488.1	c.*57-1119G>A		intron_variant	Intron 1 of 2			ENSP00000520457.1

Frequencies

GnomAD3 genomes AF: 0.228 AC: 34583 AN: 151564 Hom.: 4800 Cov.: 31

Gnomad AFR AF: 0.396

Gnomad AMI AF: 0.132

Gnomad AMR AF: 0.140

Gnomad ASJ AF: 0.178

Gnomad EAS AF: 0.200

Gnomad SAS AF: 0.222

Gnomad FIN AF: 0.117

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.171

Gnomad OTH AF: 0.207

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

GnomAD4 genome AF: 0.228 AC: 34632 AN: 151682 Hom.: 4817 Cov.: 31 AF XY: 0.223 AC XY: 16537 AN XY: 74130

African (AFR) AF: 0.397 AC: 16352 AN: 41226

American (AMR) AF: 0.140 AC: 2135 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.178 AC: 619 AN: 3468

East Asian (EAS) AF: 0.201 AC: 1033 AN: 5150

South Asian (SAS) AF: 0.222 AC: 1064 AN: 4786

European-Finnish (FIN) AF: 0.117 AC: 1230 AN: 10542

Middle Eastern (MID) AF: 0.163 AC: 48 AN: 294

European-Non Finnish (NFE) AF: 0.171 AC: 11595 AN: 67926

Other (OTH) AF: 0.207 AC: 436 AN: 2106

Alfa AF: 0.189 Hom.: 2072

Bravo AF: 0.236

Asia WGS AF: 0.188 AC: 654 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.078
DANN	Benign	0.74
PhyloP100		-4.0

Splicing

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

Other links and lift over

dbSNP: rs1776421; hg19: chr1-53884457;