ENST00000525374.1:n.25-2747A>G

Variant names:

• chr11-105047405-T-C
• rs501626
• ENST00000525374.1:n.25-2747A>G

Variant summary

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

The ENST00000525374.1(CARD16):​n.25-2747A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0917 in 152,080 control chromosomes in the GnomAD database, including 959 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 0.092 (959 hom., cov: 32)
• Consequence: CARD16 ENST00000525374.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.129
• Publications: 3 publications found

Genes affected

CARD16 (HGNC:33701): (caspase recruitment domain family member 16) Enables several functions, including CARD domain binding activity; cysteine-type endopeptidase inhibitor activity; and enzyme binding activity. Involved in several processes, including negative regulation of cysteine-type endopeptidase activity; regulation of gene expression; and regulation of signal transduction. Part of protease inhibitor complex. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000303891 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.207 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000525374.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CARD16	ENST00000525374.1	TSL:3	n.25-2747A>G		intron	N/A
	ENSG00000303891	ENST00000797905.1		n.746-10955T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0918 AC: 13948 AN: 151962 Hom.: 958 Cov.: 32

Gnomad AFR AF: 0.0207

Gnomad AMI AF: 0.135

Gnomad AMR AF: 0.213

Gnomad ASJ AF: 0.106

Gnomad EAS AF: 0.00463

Gnomad SAS AF: 0.101

Gnomad FIN AF: 0.142

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.104

Gnomad OTH AF: 0.113

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

GnomAD4 genome AF: 0.0917 AC: 13949 AN: 152080 Hom.: 959 Cov.: 32 AF XY: 0.0964 AC XY: 7167 AN XY: 74324

African (AFR) AF: 0.0206 AC: 857 AN: 41514

American (AMR) AF: 0.213 AC: 3252 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.106 AC: 369 AN: 3470

East Asian (EAS) AF: 0.00483 AC: 25 AN: 5172

South Asian (SAS) AF: 0.101 AC: 483 AN: 4804

European-Finnish (FIN) AF: 0.142 AC: 1500 AN: 10570

Middle Eastern (MID) AF: 0.122 AC: 36 AN: 294

European-Non Finnish (NFE) AF: 0.104 AC: 7069 AN: 67972

Other (OTH) AF: 0.111 AC: 235 AN: 2108

Alfa AF: 0.0991 Hom.: 301

Bravo AF: 0.0948

Asia WGS AF: 0.0600 AC: 208 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	5.8
DANN	Benign	0.35
PhyloP100		-0.13
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs501626; hg19: chr11-104918132;