chr2-197180806-T-C

Variant names:

• chr2-197180806-T-C
• rs7570752
• NM_001195144.2:c.111+6217A>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.111+6217A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.288 in 151,970 control chromosomes in the GnomAD database, including 7,073 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 0.29 (7073 hom., cov: 31)
• Consequence: ANKRD44 NM_001195144.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.49
• Publications: 4 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=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.423 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ANKRD44	NM_001195144.2	MANE Select	c.111+6217A>G		intron	N/A	NP_001182073.1
	ANKRD44	NM_001367495.1		c.111+6217A>G		intron	N/A	NP_001354424.1
	ANKRD44	NM_001367497.1		c.111+6217A>G		intron	N/A	NP_001354426.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ANKRD44	ENST00000282272.15	TSL:5 MANE Select	c.111+6217A>G		intron	N/A	ENSP00000282272.9
	ANKRD44	ENST00000409919.5	TSL:1	c.111+6217A>G		intron	N/A	ENSP00000387233.1
	ANKRD44	ENST00000647377.1		c.111+6217A>G		intron	N/A	ENSP00000496628.1

Frequencies

GnomAD3 genomes AF: 0.288 AC: 43723 AN: 151852 Hom.: 7071 Cov.: 31

Gnomad AFR AF: 0.428

Gnomad AMI AF: 0.304

Gnomad AMR AF: 0.199

Gnomad ASJ AF: 0.219

Gnomad EAS AF: 0.0807

Gnomad SAS AF: 0.230

Gnomad FIN AF: 0.267

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.250

Gnomad OTH AF: 0.260

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

GnomAD4 genome AF: 0.288 AC: 43748 AN: 151970 Hom.: 7073 Cov.: 31 AF XY: 0.288 AC XY: 21376 AN XY: 74268

African (AFR) AF: 0.428 AC: 17746 AN: 41452

American (AMR) AF: 0.199 AC: 3036 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.219 AC: 761 AN: 3470

East Asian (EAS) AF: 0.0798 AC: 413 AN: 5178

South Asian (SAS) AF: 0.230 AC: 1107 AN: 4804

European-Finnish (FIN) AF: 0.267 AC: 2810 AN: 10518

Middle Eastern (MID) AF: 0.282 AC: 83 AN: 294

European-Non Finnish (NFE) AF: 0.250 AC: 16973 AN: 67974

Other (OTH) AF: 0.258 AC: 543 AN: 2106

Alfa AF: 0.259 Hom.: 3458

Bravo AF: 0.288

Asia WGS AF: 0.189 AC: 657 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.30
DANN	Benign	0.72
PhyloP100		-1.5
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: rs7570752; hg19: chr2-198045530;