13-106411177-C-T

Variant names:

• chr13-106411177-C-T
• rs11843540
• ENST00000753311.1:n.148+6391G>A

Variant summary

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

The ENST00000753311.1(ENSG00000298145):​n.148+6391G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.072 in 152,122 control chromosomes in the GnomAD database, including 527 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 0.072 (527 hom., cov: 32)
• Consequence: ENSG00000298145 ENST00000753311.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.149
• Publications: 1 publications found

Genes affected

ENSG00000298145 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.14 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
ENSG00000298145	ENST00000753311.1	n.148+6391G>A		intron_variant	Intron 1 of 1
ENSG00000298164	ENST00000753443.1	n.266+3267C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.0718 AC: 10918 AN: 152004 Hom.: 524 Cov.: 32

Gnomad AFR AF: 0.143

Gnomad AMI AF: 0.0286

Gnomad AMR AF: 0.0760

Gnomad ASJ AF: 0.0334

Gnomad EAS AF: 0.000771

Gnomad SAS AF: 0.0216

Gnomad FIN AF: 0.0795

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0390

Gnomad OTH AF: 0.0473

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

GnomAD4 genome AF: 0.0720 AC: 10948 AN: 152122 Hom.: 527 Cov.: 32 AF XY: 0.0712 AC XY: 5294 AN XY: 74372

African (AFR) AF: 0.143 AC: 5938 AN: 41460

American (AMR) AF: 0.0761 AC: 1162 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.0334 AC: 116 AN: 3472

East Asian (EAS) AF: 0.000773 AC: 4 AN: 5174

South Asian (SAS) AF: 0.0212 AC: 102 AN: 4814

European-Finnish (FIN) AF: 0.0795 AC: 842 AN: 10596

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.0390 AC: 2653 AN: 68008

Other (OTH) AF: 0.0463 AC: 98 AN: 2116

Alfa AF: 0.0426 Hom.: 386

Bravo AF: 0.0760

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.21
DANN	Benign	0.38
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs11843540; hg19: chr13-107063525;