rs2579411

chr2-197191959-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.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

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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.726 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ANKRD44	NM_001195144.2	c.28-4853A>G		intron_variant		ENST00000282272.15

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ANKRD44	ENST00000282272.15	c.28-4853A>G		intron_variant		5	NM_001195144.2	P4

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

Gnomad4 AFR AF: 0.733

Gnomad4 AMR AF: 0.264

Gnomad4 ASJ AF: 0.277

Gnomad4 EAS AF: 0.115

Gnomad4 SAS AF: 0.270

Gnomad4 FIN AF: 0.275

Gnomad4 NFE AF: 0.276

Gnomad4 OTH AF: 0.347

Alfa AF: 0.306 Hom.: 3670

Bravo AF: 0.409

Asia WGS AF: 0.239 AC: 833 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	1.8
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: rs2579411; hg19: chr2-198056683;