13-37461052-C-T

Variant names:

• chr13-37461052-C-T
• rs1590305
• ENST00000827669.1:n.223-17553C>T

Variant summary

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

The ENST00000827669.1(ENSG00000307651):​n.223-17553C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.206 in 152,038 control chromosomes in the GnomAD database, including 4,373 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 0.21 (4373 hom., cov: 32)
• Consequence: ENSG00000307651 ENST00000827669.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.486
• Publications: 10 publications found

Genes affected

ENSG00000307651 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.37 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000827669.1. 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
	ENSG00000307651	ENST00000827669.1		n.223-17553C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.206 AC: 31234 AN: 151920 Hom.: 4367 Cov.: 32

Gnomad AFR AF: 0.375

Gnomad AMI AF: 0.106

Gnomad AMR AF: 0.183

Gnomad ASJ AF: 0.150

Gnomad EAS AF: 0.380

Gnomad SAS AF: 0.311

Gnomad FIN AF: 0.0998

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.108

Gnomad OTH AF: 0.188

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

GnomAD4 genome AF: 0.206 AC: 31266 AN: 152038 Hom.: 4373 Cov.: 32 AF XY: 0.209 AC XY: 15531 AN XY: 74340

African (AFR) AF: 0.375 AC: 15563 AN: 41460

American (AMR) AF: 0.184 AC: 2802 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.150 AC: 520 AN: 3464

East Asian (EAS) AF: 0.379 AC: 1954 AN: 5160

South Asian (SAS) AF: 0.310 AC: 1496 AN: 4820

European-Finnish (FIN) AF: 0.0998 AC: 1057 AN: 10592

Middle Eastern (MID) AF: 0.252 AC: 74 AN: 294

European-Non Finnish (NFE) AF: 0.108 AC: 7311 AN: 67960

Other (OTH) AF: 0.186 AC: 393 AN: 2112

Alfa AF: 0.152 Hom.: 4391

Bravo AF: 0.219

Asia WGS AF: 0.314 AC: 1094 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	4.2
DANN	Benign	0.51
PhyloP100		-0.49

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1590305;

hg19: chr13-38035189;