2-197180806-T-C

Position:

• chr2-197180806-T-C

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ANKRD44	NM_001195144.2	c.111+6217A>G		intron_variant		ENST00000282272.15	NP_001182073.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ANKRD44	ENST00000282272.15	c.111+6217A>G		intron_variant		5	NM_001195144.2	ENSP00000282272	P4

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

Gnomad4 AFR AF: 0.428

Gnomad4 AMR AF: 0.199

Gnomad4 ASJ AF: 0.219

Gnomad4 EAS AF: 0.0798

Gnomad4 SAS AF: 0.230

Gnomad4 FIN AF: 0.267

Gnomad4 NFE AF: 0.250

Gnomad4 OTH AF: 0.258

Alfa AF: 0.259 Hom.: 3148

Bravo AF: 0.288

Asia WGS AF: 0.189 AC: 657 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.30
DANN	Benign	0.72

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

Publications

LitVar

Other links and lift over

dbSNP: rs7570752; hg19: chr2-198045530;