1-36524039-G-A

Variant names:

• chr1-36524039-G-A
• rs4462101
• ENST00000747486.1:n.278+24400G>A

Variant summary

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

The ENST00000747486.1(ENSG00000297367):​n.278+24400G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.11 in 152,258 control chromosomes in the GnomAD database, including 1,122 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 0.11 (1122 hom., cov: 33)
• Consequence: ENSG00000297367 ENST00000747486.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.27
• Publications: 4 publications found

Genes affected

ENSG00000297367 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.177 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000747486.1. 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
	ENSG00000297367	ENST00000747486.1		n.278+24400G>A		intron	N/A
	ENSG00000297367	ENST00000747487.1		n.363-32597G>A		intron	N/A
	ENSG00000297367	ENST00000747488.1		n.211-3442G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.110 AC: 16726 AN: 152140 Hom.: 1123 Cov.: 33

Gnomad AFR AF: 0.0336

Gnomad AMI AF: 0.0768

Gnomad AMR AF: 0.117

Gnomad ASJ AF: 0.132

Gnomad EAS AF: 0.0296

Gnomad SAS AF: 0.186

Gnomad FIN AF: 0.167

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.145

Gnomad OTH AF: 0.133

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

GnomAD4 genome AF: 0.110 AC: 16720 AN: 152258 Hom.: 1122 Cov.: 33 AF XY: 0.112 AC XY: 8344 AN XY: 74452

African (AFR) AF: 0.0335 AC: 1393 AN: 41562

American (AMR) AF: 0.117 AC: 1787 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.132 AC: 458 AN: 3470

East Asian (EAS) AF: 0.0291 AC: 151 AN: 5194

South Asian (SAS) AF: 0.187 AC: 901 AN: 4824

European-Finnish (FIN) AF: 0.167 AC: 1771 AN: 10576

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.145 AC: 9867 AN: 68022

Other (OTH) AF: 0.133 AC: 280 AN: 2112

Alfa AF: 0.138 Hom.: 836

Bravo AF: 0.0988

Asia WGS AF: 0.137 AC: 475 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	13
DANN	Benign	0.60
PhyloP100		3.3

Splicing

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

Other links and lift over

dbSNP: rs4462101; hg19: chr1-36989640;