rs10497804

Positions:

• chr2-197190234-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001195144.2(ANKRD44):​c.28-3128T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.224 in 152,108 control chromosomes in the GnomAD database, including 3,997 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 0.22 (3997 hom., cov: 32)
• Consequence: ANKRD44 NM_001195144.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.863

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=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.245 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ANKRD44	NM_001195144.2	c.28-3128T>C		intron_variant		ENST00000282272.15

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ANKRD44	ENST00000282272.15	c.28-3128T>C		intron_variant		5	NM_001195144.2	P4

Frequencies

GnomAD3 genomes AF: 0.224 AC: 34015 AN: 151988 Hom.: 4000 Cov.: 32

Gnomad AFR AF: 0.208

Gnomad AMI AF: 0.302

Gnomad AMR AF: 0.172

Gnomad ASJ AF: 0.216

Gnomad EAS AF: 0.0812

Gnomad SAS AF: 0.229

Gnomad FIN AF: 0.267

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.249

Gnomad OTH AF: 0.205

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

GnomAD4 genome AF: 0.224 AC: 34015 AN: 152108 Hom.: 3997 Cov.: 32 AF XY: 0.225 AC XY: 16716 AN XY: 74348

Gnomad4 AFR AF: 0.208

Gnomad4 AMR AF: 0.172

Gnomad4 ASJ AF: 0.216

Gnomad4 EAS AF: 0.0803

Gnomad4 SAS AF: 0.229

Gnomad4 FIN AF: 0.267

Gnomad4 NFE AF: 0.249

Gnomad4 OTH AF: 0.204

Alfa AF: 0.235 Hom.: 982

Bravo AF: 0.214

Asia WGS AF: 0.177 AC: 617 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	5.2
DANN	Benign	0.65

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: rs10497804; hg19: chr2-198054958;