rs2579411

Variant names:

• chr2-197191959-T-C
• rs2579411
• NM_001195144.2:c.28-4853A>G

Variant summary

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

The NM_001195144.2(ANKRD44):​c.28-4853A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.395 in 151,986 control chromosomes in the GnomAD database, including 15,318 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 0.39 (15318 hom., cov: 31)
• Consequence: ANKRD44 NM_001195144.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.953
• Publications: 1 publications found

Genes affected

ANKRD44 (HGNC:25259): (ankyrin repeat domain 44)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.726 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001195144.2. 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
	ANKRD44	NM_001195144.2	MANE Select	c.28-4853A>G		intron	N/A	NP_001182073.1	Q8N8A2-1
	ANKRD44	NM_001367495.1		c.28-4853A>G		intron	N/A	NP_001354424.1
	ANKRD44	NM_001367497.1		c.28-4853A>G		intron	N/A	NP_001354426.1	A0A2R8Y7Y4

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ANKRD44	ENST00000282272.15	TSL:5 MANE Select	c.28-4853A>G		intron	N/A	ENSP00000282272.9	Q8N8A2-1
	ANKRD44	ENST00000409919.5	TSL:1	c.28-4853A>G		intron	N/A	ENSP00000387233.1	Q8N8A2-5
	ANKRD44	ENST00000647377.1		c.28-4853A>G		intron	N/A	ENSP00000496628.1	A0A2R8Y7Y4

Frequencies

GnomAD3 genomes AF: 0.394 AC: 59911 AN: 151870 Hom.: 15289 Cov.: 31

Gnomad AFR AF: 0.733

Gnomad AMI AF: 0.316

Gnomad AMR AF: 0.265

Gnomad ASJ AF: 0.277

Gnomad EAS AF: 0.116

Gnomad SAS AF: 0.269

Gnomad FIN AF: 0.275

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.276

Gnomad OTH AF: 0.350

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

GnomAD4 genome AF: 0.395 AC: 59989 AN: 151986 Hom.: 15318 Cov.: 31 AF XY: 0.390 AC XY: 28951 AN XY: 74286

African (AFR) AF: 0.733 AC: 30365 AN: 41434

American (AMR) AF: 0.264 AC: 4039 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.277 AC: 960 AN: 3468

East Asian (EAS) AF: 0.115 AC: 595 AN: 5176

South Asian (SAS) AF: 0.270 AC: 1299 AN: 4816

European-Finnish (FIN) AF: 0.275 AC: 2896 AN: 10540

Middle Eastern (MID) AF: 0.310 AC: 91 AN: 294

European-Non Finnish (NFE) AF: 0.276 AC: 18723 AN: 67958

Other (OTH) AF: 0.347 AC: 733 AN: 2112

Alfa AF: 0.308 Hom.: 4204

Bravo AF: 0.409

Asia WGS AF: 0.239 AC: 833 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.8
DANN	Benign	0.65
PhyloP100		-0.95
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: rs2579411; hg19: chr2-198056683;