2-197279278-A-G

Variant names:

• chr2-197279278-A-G
• rs1429411
• NM_001195144.2:c.27+31300T>C

Variant summary

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

The NM_001195144.2(ANKRD44):​c.27+31300T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.341 in 152,050 control chromosomes in the GnomAD database, including 11,107 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 0.34 (11107 hom., cov: 31)
• Consequence: ANKRD44 NM_001195144.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.332
• Publications: 12 publications found

Genes affected

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

ANKRD44-IT1 (HGNC:41477): (ANKRD44 intronic transcript 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.576 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.27+31300T>C		intron	N/A	NP_001182073.1
	ANKRD44	NM_001367495.1		c.27+31300T>C		intron	N/A	NP_001354424.1
	ANKRD44	NM_001367497.1		c.27+31300T>C		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.27+31300T>C		intron	N/A	ENSP00000282272.9
	ANKRD44	ENST00000409919.5	TSL:1	c.27+31300T>C		intron	N/A	ENSP00000387233.1
	ANKRD44-IT1	ENST00000428191.1	TSL:1	n.934+17027T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.341 AC: 51827 AN: 151930 Hom.: 11101 Cov.: 31

Gnomad AFR AF: 0.0878

Gnomad AMI AF: 0.333

Gnomad AMR AF: 0.477

Gnomad ASJ AF: 0.308

Gnomad EAS AF: 0.594

Gnomad SAS AF: 0.333

Gnomad FIN AF: 0.557

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.415

Gnomad OTH AF: 0.335

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

GnomAD4 genome AF: 0.341 AC: 51834 AN: 152050 Hom.: 11107 Cov.: 31 AF XY: 0.350 AC XY: 26044 AN XY: 74328

African (AFR) AF: 0.0876 AC: 3635 AN: 41516

American (AMR) AF: 0.478 AC: 7303 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.308 AC: 1068 AN: 3470

East Asian (EAS) AF: 0.593 AC: 3067 AN: 5168

South Asian (SAS) AF: 0.332 AC: 1600 AN: 4820

European-Finnish (FIN) AF: 0.557 AC: 5868 AN: 10542

Middle Eastern (MID) AF: 0.190 AC: 56 AN: 294

European-Non Finnish (NFE) AF: 0.415 AC: 28228 AN: 67938

Other (OTH) AF: 0.335 AC: 706 AN: 2110

Alfa AF: 0.388 Hom.: 26183

Bravo AF: 0.326

Asia WGS AF: 0.447 AC: 1553 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	8.3
DANN	Benign	0.61
PhyloP100		0.33
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs1429411; hg19: chr2-198144002;