chr13-43897181-C-T

Variant names:

• chr13-43897181-C-T
• rs2121037
• ENST00000627615.1:n.*284+5611C>T

Variant summary

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

The ENST00000627615.1(ENSG00000281883):​n.*284+5611C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.2 in 152,036 control chromosomes in the GnomAD database, including 3,126 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 0.20 (3126 hom., cov: 31)
• Consequence: ENSG00000281883 ENST00000627615.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0310
• Publications: 9 publications found

Genes affected

ENSG00000281883 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.243 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
ENSG00000281883	ENST00000627615.1	n.*284+5611C>T		intron_variant	Intron 4 of 12	5		ENSP00000486083.1

Frequencies

GnomAD3 genomes AF: 0.200 AC: 30369 AN: 151918 Hom.: 3121 Cov.: 31

Gnomad AFR AF: 0.247

Gnomad AMI AF: 0.104

Gnomad AMR AF: 0.198

Gnomad ASJ AF: 0.316

Gnomad EAS AF: 0.138

Gnomad SAS AF: 0.162

Gnomad FIN AF: 0.161

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.180

Gnomad OTH AF: 0.198

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

GnomAD4 genome AF: 0.200 AC: 30387 AN: 152036 Hom.: 3126 Cov.: 31 AF XY: 0.198 AC XY: 14749 AN XY: 74312

African (AFR) AF: 0.247 AC: 10226 AN: 41422

American (AMR) AF: 0.197 AC: 3014 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.316 AC: 1098 AN: 3470

East Asian (EAS) AF: 0.139 AC: 718 AN: 5168

South Asian (SAS) AF: 0.163 AC: 787 AN: 4824

European-Finnish (FIN) AF: 0.161 AC: 1704 AN: 10578

Middle Eastern (MID) AF: 0.231 AC: 68 AN: 294

European-Non Finnish (NFE) AF: 0.180 AC: 12259 AN: 67978

Other (OTH) AF: 0.198 AC: 418 AN: 2112

Alfa AF: 0.193 Hom.: 5724

Bravo AF: 0.206

Asia WGS AF: 0.141 AC: 487 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.4
DANN	Benign	0.74
PhyloP100		0.031

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs2121037; hg19: chr13-44471317;