1-182052148-C-T

Variant names:

• chr1-182052148-C-T
• rs7554182
• ENST00000756799.1:n.154+22549C>T

Variant summary

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

The ENST00000756799.1(ENSG00000225982):​n.154+22549C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0848 in 152,172 control chromosomes in the GnomAD database, including 1,183 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 0.085 (1183 hom., cov: 32)
• Consequence: ENSG00000225982 ENST00000756799.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0610
• Publications: 5 publications found

Genes affected

ENSG00000225982 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.58).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.214 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000756799.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000225982	ENST00000756799.1		n.154+22549C>T		intron	N/A
	ENSG00000225982	ENST00000756800.1		n.131+22549C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0846 AC: 12869 AN: 152054 Hom.: 1174 Cov.: 32

Gnomad AFR AF: 0.218

Gnomad AMI AF: 0.0143

Gnomad AMR AF: 0.0564

Gnomad ASJ AF: 0.0260

Gnomad EAS AF: 0.0575

Gnomad SAS AF: 0.223

Gnomad FIN AF: 0.0161

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0175

Gnomad OTH AF: 0.0712

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

GnomAD4 genome AF: 0.0848 AC: 12904 AN: 152172 Hom.: 1183 Cov.: 32 AF XY: 0.0862 AC XY: 6410 AN XY: 74400

African (AFR) AF: 0.218 AC: 9042 AN: 41484

American (AMR) AF: 0.0562 AC: 860 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0260 AC: 90 AN: 3466

East Asian (EAS) AF: 0.0571 AC: 296 AN: 5186

South Asian (SAS) AF: 0.222 AC: 1070 AN: 4812

European-Finnish (FIN) AF: 0.0161 AC: 171 AN: 10590

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.0175 AC: 1188 AN: 68022

Other (OTH) AF: 0.0705 AC: 149 AN: 2114

Alfa AF: 0.0322 Hom.: 431

Bravo AF: 0.0905

Asia WGS AF: 0.152 AC: 527 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.58
CADD	Benign	14
DANN	Benign	0.84
PhyloP100		-0.061

Splicing

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

Other links and lift over

dbSNP: rs7554182; hg19: chr1-182021283;