rs7934239

Variant names:

• chr11-105047790-G-A
• rs7934239
• ENST00000525374.1:n.25-3132C>T

Your query was ambiguous. Multiple possible variants found:

• chr11-105047790-G-A
• chr11-105047790-G-T

Variant summary

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

The ENST00000525374.1(CARD16):​n.25-3132C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0517 in 152,068 control chromosomes in the GnomAD database, including 204 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 0.052 (204 hom., cov: 32)
• Consequence: CARD16 ENST00000525374.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.301
• Publications: 4 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=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0615 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CARD16	ENST00000525374.1	TSL:3	n.25-3132C>T		intron	N/A
	ENSG00000303891	ENST00000797905.1		n.746-10570G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0516 AC: 7847 AN: 151950 Hom.: 204 Cov.: 32

Gnomad AFR AF: 0.0440

Gnomad AMI AF: 0.149

Gnomad AMR AF: 0.0299

Gnomad ASJ AF: 0.0577

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0106

Gnomad FIN AF: 0.0757

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0630

Gnomad OTH AF: 0.0446

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

GnomAD4 genome AF: 0.0517 AC: 7856 AN: 152068 Hom.: 204 Cov.: 32 AF XY: 0.0501 AC XY: 3726 AN XY: 74314

African (AFR) AF: 0.0441 AC: 1831 AN: 41486

American (AMR) AF: 0.0299 AC: 456 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.0577 AC: 200 AN: 3466

East Asian (EAS) AF: 0.00 AC: 0 AN: 5182

South Asian (SAS) AF: 0.0106 AC: 51 AN: 4816

European-Finnish (FIN) AF: 0.0757 AC: 799 AN: 10550

Middle Eastern (MID) AF: 0.0136 AC: 4 AN: 294

European-Non Finnish (NFE) AF: 0.0630 AC: 4286 AN: 67984

Other (OTH) AF: 0.0441 AC: 93 AN: 2108

Alfa AF: 0.0535 Hom.: 438

Bravo AF: 0.0488

Asia WGS AF: 0.00925 AC: 32 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.32
DANN	Benign	0.54
PhyloP100		-0.30
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: rs7934239; hg19: chr11-104918517;