rs2376100

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ANKRD44	XM_005246948.3	c.2978-1360A>G		intron_variant	Intron 27 of 27		XP_005247005.1
ANKRD44	XM_047446287.1	c.2924-1360A>G		intron_variant	Intron 27 of 27		XP_047302243.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ANKRD44	ENST00000424317.5	c.2369-1360A>G		intron_variant	Intron 21 of 21	1		ENSP00000403415.1

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

Gnomad4 AFR AF: 0.188

Gnomad4 AMR AF: 0.161

Gnomad4 ASJ AF: 0.168

Gnomad4 EAS AF: 0.144

Gnomad4 SAS AF: 0.135

Gnomad4 FIN AF: 0.197

Gnomad4 NFE AF: 0.148

Gnomad4 OTH AF: 0.155

Alfa AF: 0.154 Hom.: 1122

Bravo AF: 0.167

Asia WGS AF: 0.140 AC: 485 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs2376100; hg19: chr2-197833530;