2-197055445-C-T

Position:

• chr2-197055445-C-T

Variant summary

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

The NM_001195144.2(ANKRD44):​c.1650+23258G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.716 in 152,066 control chromosomes in the GnomAD database, including 40,502 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 0.72 (40502 hom., cov: 31)
• Consequence: ANKRD44 NM_001195144.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.28

Genes affected

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

ANKRD44 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.843 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ANKRD44	NM_001195144.2	c.1650+23258G>A		intron_variant		ENST00000282272.15	NP_001182073.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ANKRD44	ENST00000282272.15	c.1650+23258G>A		intron_variant		5	NM_001195144.2	ENSP00000282272.9

Frequencies

GnomAD3 genomes AF: 0.716 AC: 108779 AN: 151948 Hom.: 40495 Cov.: 31

Gnomad AFR AF: 0.491

Gnomad AMI AF: 0.675

Gnomad AMR AF: 0.789

Gnomad ASJ AF: 0.802

Gnomad EAS AF: 0.864

Gnomad SAS AF: 0.787

Gnomad FIN AF: 0.863

Gnomad MID AF: 0.745

Gnomad NFE AF: 0.792

Gnomad OTH AF: 0.738

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

GnomAD4 genome AF: 0.716 AC: 108827 AN: 152066 Hom.: 40502 Cov.: 31 AF XY: 0.720 AC XY: 53513 AN XY: 74348

Gnomad4 AFR AF: 0.491

Gnomad4 AMR AF: 0.789

Gnomad4 ASJ AF: 0.802

Gnomad4 EAS AF: 0.864

Gnomad4 SAS AF: 0.787

Gnomad4 FIN AF: 0.863

Gnomad4 NFE AF: 0.792

Gnomad4 OTH AF: 0.741

Alfa AF: 0.782 Hom.: 93444

Bravo AF: 0.700

Asia WGS AF: 0.802 AC: 2779 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.65
DANN	Benign	0.38

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: rs4850410; hg19: chr2-197920169;