chr2-197194756-A-G

Variant names:

• chr2-197194756-A-G
• rs6711427
• NM_001195144.2:c.28-7650T>C

Variant summary

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

The NM_001195144.2(ANKRD44):​c.28-7650T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.218 in 152,176 control chromosomes in the GnomAD database, including 3,816 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 (3816 hom., cov: 32)
• Consequence: ANKRD44 NM_001195144.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.09
• Publications: 0 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=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.245 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ANKRD44	NM_001195144.2	c.28-7650T>C		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.28-7650T>C		intron_variant	Intron 1 of 27	5	NM_001195144.2	ENSP00000282272.9

Frequencies

GnomAD3 genomes AF: 0.218 AC: 33127 AN: 152058 Hom.: 3820 Cov.: 32

Gnomad AFR AF: 0.188

Gnomad AMI AF: 0.304

Gnomad AMR AF: 0.170

Gnomad ASJ AF: 0.215

Gnomad EAS AF: 0.0812

Gnomad SAS AF: 0.230

Gnomad FIN AF: 0.266

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.248

Gnomad OTH AF: 0.202

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

GnomAD4 genome AF: 0.218 AC: 33122 AN: 152176 Hom.: 3816 Cov.: 32 AF XY: 0.219 AC XY: 16286 AN XY: 74398

African (AFR) AF: 0.188 AC: 7786 AN: 41508

American (AMR) AF: 0.169 AC: 2589 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.215 AC: 746 AN: 3468

East Asian (EAS) AF: 0.0804 AC: 417 AN: 5188

South Asian (SAS) AF: 0.230 AC: 1109 AN: 4832

European-Finnish (FIN) AF: 0.266 AC: 2813 AN: 10562

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

European-Non Finnish (NFE) AF: 0.248 AC: 16882 AN: 68002

Other (OTH) AF: 0.200 AC: 423 AN: 2110

Alfa AF: 0.233 Hom.: 540

Bravo AF: 0.208

Asia WGS AF: 0.175 AC: 609 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	4.9
DANN	Benign	0.58
PhyloP100		1.1
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: rs6711427; hg19: chr2-198059480;