13-106416281-C-T

Variant names:

• chr13-106416281-C-T
• rs1322740
• ENST00000753311.1:n.148+1287G>A

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000753311.1(ENSG00000298145):​n.148+1287G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.27 in 152,132 control chromosomes in the GnomAD database, including 6,201 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 0.27 (6201 hom., cov: 33)
• Consequence: ENSG00000298145 ENST00000753311.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.839
• Publications: 1 publications found

Genes affected

ENSG00000298145 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.33).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.387 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000753311.1. 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
	ENSG00000298145	ENST00000753311.1		n.148+1287G>A		intron	N/A
	ENSG00000298164	ENST00000753443.1		n.267-1270C>T		intron	N/A
	ENSG00000298177	ENST00000753680.1		n.33+491G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.270 AC: 41065 AN: 152016 Hom.: 6203 Cov.: 33

Gnomad AFR AF: 0.393

Gnomad AMI AF: 0.167

Gnomad AMR AF: 0.345

Gnomad ASJ AF: 0.243

Gnomad EAS AF: 0.298

Gnomad SAS AF: 0.266

Gnomad FIN AF: 0.150

Gnomad MID AF: 0.360

Gnomad NFE AF: 0.197

Gnomad OTH AF: 0.296

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

GnomAD4 genome AF: 0.270 AC: 41093 AN: 152132 Hom.: 6201 Cov.: 33 AF XY: 0.269 AC XY: 19987 AN XY: 74366

African (AFR) AF: 0.392 AC: 16274 AN: 41498

American (AMR) AF: 0.346 AC: 5282 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.243 AC: 842 AN: 3470

East Asian (EAS) AF: 0.298 AC: 1544 AN: 5178

South Asian (SAS) AF: 0.265 AC: 1276 AN: 4822

European-Finnish (FIN) AF: 0.150 AC: 1585 AN: 10592

Middle Eastern (MID) AF: 0.349 AC: 102 AN: 292

European-Non Finnish (NFE) AF: 0.197 AC: 13415 AN: 67980

Other (OTH) AF: 0.294 AC: 621 AN: 2114

Alfa AF: 0.228 Hom.: 6820

Bravo AF: 0.293

Asia WGS AF: 0.281 AC: 977 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.33
CADD	Benign	15
DANN	Benign	0.61
PhyloP100		0.84

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: rs1322740;

hg19: chr13-107068629;