chr2-197055445-C-T

Variant names:

• chr2-197055445-C-T
• rs4850410
• NM_001195144.2:c.1650+23258G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 12 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

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.1650+23258G>A		intron	N/A	NP_001182073.1
	ANKRD44	NM_001367495.1		c.1704+23258G>A		intron	N/A	NP_001354424.1
	ANKRD44	NM_001367497.1		c.1650+23258G>A		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.1650+23258G>A		intron	N/A	ENSP00000282272.9
	ANKRD44	ENST00000424317.5	TSL:1	c.1095+23258G>A		intron	N/A	ENSP00000403415.1
	ANKRD44	ENST00000647377.1		c.1650+23258G>A		intron	N/A	ENSP00000496628.1

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

African (AFR) AF: 0.491 AC: 20348 AN: 41422

American (AMR) AF: 0.789 AC: 12063 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.802 AC: 2785 AN: 3472

East Asian (EAS) AF: 0.864 AC: 4476 AN: 5178

South Asian (SAS) AF: 0.787 AC: 3799 AN: 4826

European-Finnish (FIN) AF: 0.863 AC: 9139 AN: 10584

Middle Eastern (MID) AF: 0.740 AC: 216 AN: 292

European-Non Finnish (NFE) AF: 0.792 AC: 53821 AN: 67976

Other (OTH) AF: 0.741 AC: 1564 AN: 2112

Alfa AF: 0.771 Hom.: 191739

Bravo AF: 0.700

Asia WGS AF: 0.802 AC: 2779 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.65
DANN	Benign	0.38
PhyloP100		-1.3
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs4850410; hg19: chr2-197920169;