NM_001300975.2:c.587-6320C>T

Variant names:

• chr11-83218535-C-T
• rs12225692
• NM_001300975.2:c.587-6320C>T

Variant summary

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

The NM_001300975.2(ANKRD42):​c.587-6320C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0897 in 152,170 control chromosomes in the GnomAD database, including 800 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 0.090 (800 hom., cov: 32)
• Consequence: ANKRD42 NM_001300975.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.989
• Publications: 0 publications found

Genes affected

ANKRD42 (HGNC:26752): (ankyrin repeat domain 42) Predicted to enable NF-kappaB binding activity. Predicted to act upstream of or within positive regulation of NF-kappaB transcription factor activity and positive regulation of cytokine production involved in inflammatory response. Predicted to be located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.151 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001300975.2. 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
	ANKRD42	NM_001300975.2	MANE Select	c.587-6320C>T		intron	N/A	NP_001287904.1	E9PIL2
	ANKRD42	NM_001433541.1		c.584-6320C>T		intron	N/A	NP_001420470.1
	ANKRD42	NM_001300973.2		c.584-6320C>T		intron	N/A	NP_001287902.1	F8W6I9

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ANKRD42	ENST00000533342.6	TSL:1 MANE Select	c.587-6320C>T		intron	N/A	ENSP00000435790.1	E9PIL2
	ANKRD42	ENST00000260047.10	TSL:1	c.584-6320C>T		intron	N/A	ENSP00000260047.6	F8W6I9
	ANKRD42	ENST00000531895.5	TSL:1	c.587-6320C>T		intron	N/A	ENSP00000434666.1	E9PP91

Frequencies

GnomAD3 genomes AF: 0.0896 AC: 13622 AN: 152052 Hom.: 796 Cov.: 32

Gnomad AFR AF: 0.154

Gnomad AMI AF: 0.00989

Gnomad AMR AF: 0.0633

Gnomad ASJ AF: 0.0841

Gnomad EAS AF: 0.0296

Gnomad SAS AF: 0.107

Gnomad FIN AF: 0.0283

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.0703

Gnomad OTH AF: 0.0908

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

GnomAD4 genome AF: 0.0897 AC: 13647 AN: 152170 Hom.: 800 Cov.: 32 AF XY: 0.0863 AC XY: 6419 AN XY: 74414

African (AFR) AF: 0.154 AC: 6405 AN: 41482

American (AMR) AF: 0.0633 AC: 968 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0841 AC: 292 AN: 3470

East Asian (EAS) AF: 0.0293 AC: 152 AN: 5188

South Asian (SAS) AF: 0.107 AC: 515 AN: 4830

European-Finnish (FIN) AF: 0.0283 AC: 300 AN: 10598

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.0703 AC: 4778 AN: 67984

Other (OTH) AF: 0.0899 AC: 190 AN: 2114

Alfa AF: 0.0774 Hom.: 190

Bravo AF: 0.0941

Asia WGS AF: 0.0820 AC: 285 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	7.1
DANN	Benign	0.91
PhyloP100		-0.99
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs12225692; hg19: chr11-82929577;