13-103247149-C-A

Variant names:

• chr13-103247149-C-A
• rs16961766
• ENST00000741727.1:n.105-48857C>A

Variant summary

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

The ENST00000741727.1(ENSG00000296764):​n.105-48857C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0531 in 152,284 control chromosomes in the GnomAD database, including 410 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 0.053 (410 hom., cov: 32)
• Consequence: ENSG00000296764 ENST00000741727.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.688
• Publications: 2 publications found

Genes affected

ENSG00000296764 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.37).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.115 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000741727.1. 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
	ENSG00000296764	ENST00000741727.1		n.105-48857C>A		intron	N/A
	ENSG00000296764	ENST00000741728.1		n.100-48857C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0531 AC: 8073 AN: 152166 Hom.: 409 Cov.: 32

Gnomad AFR AF: 0.118

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0616

Gnomad ASJ AF: 0.0265

Gnomad EAS AF: 0.103

Gnomad SAS AF: 0.101

Gnomad FIN AF: 0.0266

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0109

Gnomad OTH AF: 0.0478

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

GnomAD4 genome AF: 0.0531 AC: 8081 AN: 152284 Hom.: 410 Cov.: 32 AF XY: 0.0549 AC XY: 4087 AN XY: 74464

African (AFR) AF: 0.118 AC: 4888 AN: 41546

American (AMR) AF: 0.0615 AC: 941 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.0265 AC: 92 AN: 3468

East Asian (EAS) AF: 0.103 AC: 535 AN: 5182

South Asian (SAS) AF: 0.101 AC: 487 AN: 4828

European-Finnish (FIN) AF: 0.0266 AC: 282 AN: 10608

Middle Eastern (MID) AF: 0.0544 AC: 16 AN: 294

European-Non Finnish (NFE) AF: 0.0109 AC: 740 AN: 68024

Other (OTH) AF: 0.0473 AC: 100 AN: 2116

Alfa AF: 0.0237 Hom.: 199

Bravo AF: 0.0570

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.37
CADD	Benign	13
DANN	Benign	0.54
PhyloP100		0.69

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: rs16961766;

hg19: chr13-103899499;