1-36732751-T-C

Variant names:

• chr1-36732751-T-C
• rs7549591
• ENST00000724118.1:n.198+4236T>C

Variant summary

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

The ENST00000724118.1(ENSG00000234481):​n.198+4236T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.398 in 151,790 control chromosomes in the GnomAD database, including 12,684 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 0.40 (12684 hom., cov: 33)
• Consequence: ENSG00000234481 ENST00000724118.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.24
• Publications: 3 publications found

Genes affected

ENSG00000234481 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.605 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000724118.1. 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
	ENSG00000234481	ENST00000724118.1		n.198+4236T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.398 AC: 60297 AN: 151672 Hom.: 12670 Cov.: 33

Gnomad AFR AF: 0.515

Gnomad AMI AF: 0.436

Gnomad AMR AF: 0.427

Gnomad ASJ AF: 0.274

Gnomad EAS AF: 0.623

Gnomad SAS AF: 0.391

Gnomad FIN AF: 0.312

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.323

Gnomad OTH AF: 0.391

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

GnomAD4 genome AF: 0.398 AC: 60345 AN: 151790 Hom.: 12684 Cov.: 33 AF XY: 0.398 AC XY: 29520 AN XY: 74200

African (AFR) AF: 0.514 AC: 21255 AN: 41312

American (AMR) AF: 0.428 AC: 6532 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.274 AC: 949 AN: 3468

East Asian (EAS) AF: 0.623 AC: 3204 AN: 5144

South Asian (SAS) AF: 0.391 AC: 1887 AN: 4822

European-Finnish (FIN) AF: 0.312 AC: 3295 AN: 10570

Middle Eastern (MID) AF: 0.367 AC: 108 AN: 294

European-Non Finnish (NFE) AF: 0.323 AC: 21897 AN: 67890

Other (OTH) AF: 0.391 AC: 821 AN: 2102

Alfa AF: 0.343 Hom.: 39439

Bravo AF: 0.413

Asia WGS AF: 0.515 AC: 1793 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	12
DANN	Benign	0.32
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs7549591; hg19: chr1-37198352;