chr2-197304406-T-C

Variant names:

• chr2-197304406-T-C
• rs12464356
• NM_001195144.2:c.27+6172A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001195144.2(ANKRD44):​c.27+6172A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0481 in 152,320 control chromosomes in the GnomAD database, including 252 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 0.048 (252 hom., cov: 32)
• Consequence: ANKRD44 NM_001195144.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.76
• Publications: 1 publications found

Genes affected

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

ANKRD44-IT1 (HGNC:41477): (ANKRD44 intronic transcript 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0648 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ANKRD44	NM_001195144.2	c.27+6172A>G		intron_variant	Intron 1 of 27	ENST00000282272.15	NP_001182073.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ANKRD44	ENST00000282272.15	c.27+6172A>G		intron_variant	Intron 1 of 27	5	NM_001195144.2	ENSP00000282272.9

Frequencies

GnomAD3 genomes AF: 0.0481 AC: 7320 AN: 152202 Hom.: 252 Cov.: 32

Gnomad AFR AF: 0.0105

Gnomad AMI AF: 0.0482

Gnomad AMR AF: 0.0507

Gnomad ASJ AF: 0.0369

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0246

Gnomad FIN AF: 0.113

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.0664

Gnomad OTH AF: 0.0464

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

GnomAD4 genome AF: 0.0481 AC: 7320 AN: 152320 Hom.: 252 Cov.: 32 AF XY: 0.0496 AC XY: 3697 AN XY: 74478

African (AFR) AF: 0.0105 AC: 436 AN: 41570

American (AMR) AF: 0.0507 AC: 775 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0369 AC: 128 AN: 3472

East Asian (EAS) AF: 0.00 AC: 0 AN: 5192

South Asian (SAS) AF: 0.0245 AC: 118 AN: 4826

European-Finnish (FIN) AF: 0.113 AC: 1201 AN: 10604

Middle Eastern (MID) AF: 0.0102 AC: 3 AN: 294

European-Non Finnish (NFE) AF: 0.0664 AC: 4519 AN: 68038

Other (OTH) AF: 0.0455 AC: 96 AN: 2112

Alfa AF: 0.0550 Hom.: 145

Bravo AF: 0.0425

Asia WGS AF: 0.0140 AC: 49 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.0050
DANN	Benign	0.36
PhyloP100		-3.8
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: rs12464356; hg19: chr2-198169130;