rs2376100

Variant names:

• chr2-196968806-T-C
• rs2376100
• ENST00000424317.5:c.2369-1360A>G

Variant summary

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

The ENST00000424317.5(ANKRD44):​c.2369-1360A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.164 in 152,166 control chromosomes in the GnomAD database, including 2,074 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 0.16 (2074 hom., cov: 32)
• Consequence: ANKRD44 ENST00000424317.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.686
• Publications: 6 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=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.184 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000424317.5. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ANKRD44	ENST00000424317.5	TSL:1	c.2369-1360A>G		intron	N/A	ENSP00000403415.1	H7C209

Frequencies

GnomAD3 genomes AF: 0.164 AC: 24883 AN: 152048 Hom.: 2073 Cov.: 32

Gnomad AFR AF: 0.188

Gnomad AMI AF: 0.141

Gnomad AMR AF: 0.161

Gnomad ASJ AF: 0.168

Gnomad EAS AF: 0.145

Gnomad SAS AF: 0.136

Gnomad FIN AF: 0.197

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.148

Gnomad OTH AF: 0.156

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

GnomAD4 genome AF: 0.164 AC: 24903 AN: 152166 Hom.: 2074 Cov.: 32 AF XY: 0.165 AC XY: 12286 AN XY: 74378

African (AFR) AF: 0.188 AC: 7798 AN: 41524

American (AMR) AF: 0.161 AC: 2460 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.168 AC: 584 AN: 3472

East Asian (EAS) AF: 0.144 AC: 746 AN: 5176

South Asian (SAS) AF: 0.135 AC: 653 AN: 4822

European-Finnish (FIN) AF: 0.197 AC: 2084 AN: 10578

Middle Eastern (MID) AF: 0.201 AC: 59 AN: 294

European-Non Finnish (NFE) AF: 0.148 AC: 10063 AN: 67992

Other (OTH) AF: 0.155 AC: 328 AN: 2114

Alfa AF: 0.154 Hom.: 1764

Bravo AF: 0.167

Asia WGS AF: 0.140 AC: 485 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	4.3
DANN	Benign	0.73
PhyloP100		0.69

Splicing

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: rs2376100;

hg19: chr2-197833530;