rs10497804

Variant names:

• chr2-197190234-A-G
• rs10497804
• NM_001195144.2:c.28-3128T>C

Variant summary

Our verdict is

Benign

<-10 Benign

-7

-6

-1

0

+5

+6

+9

+10

BenignB

Likely BenignLB

UncertainVUS

Likely PathogenicLP

PathogenicP

. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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
• Publications: 2 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=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.245 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ANKRD44	NM_001195144.2	MANE Select	c.28-3128T>C		intron	N/A	NP_001182073.1	Q8N8A2-1
	ANKRD44	NM_001367495.1		c.28-3128T>C		intron	N/A	NP_001354424.1
	ANKRD44	NM_001367497.1		c.28-3128T>C		intron	N/A	NP_001354426.1	A0A2R8Y7Y4

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ANKRD44	ENST00000282272.15	TSL:5 MANE Select	c.28-3128T>C		intron	N/A	ENSP00000282272.9	Q8N8A2-1
	ANKRD44	ENST00000409919.5	TSL:1	c.28-3128T>C		intron	N/A	ENSP00000387233.1	Q8N8A2-5
	ANKRD44	ENST00000647377.1		c.28-3128T>C		intron	N/A	ENSP00000496628.1	A0A2R8Y7Y4

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

African (AFR) AF: 0.208 AC: 8615 AN: 41508

American (AMR) AF: 0.172 AC: 2628 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.216 AC: 750 AN: 3470

East Asian (EAS) AF: 0.0803 AC: 417 AN: 5190

South Asian (SAS) AF: 0.229 AC: 1102 AN: 4816

European-Finnish (FIN) AF: 0.267 AC: 2823 AN: 10562

Middle Eastern (MID) AF: 0.272 AC: 80 AN: 294

European-Non Finnish (NFE) AF: 0.249 AC: 16897 AN: 67974

Other (OTH) AF: 0.204 AC: 430 AN: 2110

Alfa AF: 0.228 Hom.: 1605

Bravo AF: 0.214

Asia WGS AF: 0.177 AC: 617 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	5.2
DANN	Benign	0.65
PhyloP100		0.86
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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10497804;

hg19: chr2-198054958;

ACMG debug oncogenicity

ACGS debug oncogenicity

ACMG debug germline