rs11098171

chr4-112789017-T-Cchr4-112789017-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001386186.2(ANK2):c.72+82800T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.267 in 517,422 control chromosomes in the GnomAD database, including 22,738 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 0.31 (8634 hom., cov: 32)
  • Exomes 𝑓: 0.25 (14104 hom.)
• Consequence: ANK2 NM_001386186.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.133

Genes affected

ANK2 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.564 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ANK2	NM_001354269.3	c.72+82800T>C		intron_variant
ANK2	NM_001386148.2	c.72+82800T>C		intron_variant
ANK2	NM_001386186.2	c.72+82800T>C		intron_variant
ANK2	NM_001386187.2	c.72+82800T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.310 AC: 47045 AN: 151806 Hom.: 8614 Cov.: 32

Gnomad AFR AF: 0.474

Gnomad AMI AF: 0.221

Gnomad AMR AF: 0.354

Gnomad ASJ AF: 0.125

Gnomad EAS AF: 0.581

Gnomad SAS AF: 0.322

Gnomad FIN AF: 0.207

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.207

Gnomad OTH AF: 0.261

GnomAD4 exome AF: 0.248 AC: 90775 AN: 365498 Hom.: 14104 AF XY: 0.246 AC XY: 46641 AN XY: 189752

Gnomad4 AFR exome AF: 0.462

Gnomad4 AMR exome AF: 0.384

Gnomad4 ASJ exome AF: 0.115

Gnomad4 EAS exome AF: 0.574

Gnomad4 SAS exome AF: 0.278

Gnomad4 FIN exome AF: 0.206

Gnomad4 NFE exome AF: 0.199

Gnomad4 OTH exome AF: 0.239

GnomAD4 genome AF: 0.310 AC: 47122 AN: 151924 Hom.: 8634 Cov.: 32 AF XY: 0.313 AC XY: 23256 AN XY: 74272

Gnomad4 AFR AF: 0.474

Gnomad4 AMR AF: 0.355

Gnomad4 ASJ AF: 0.125

Gnomad4 EAS AF: 0.581

Gnomad4 SAS AF: 0.321

Gnomad4 FIN AF: 0.207

Gnomad4 NFE AF: 0.207

Gnomad4 OTH AF: 0.260

Alfa AF: 0.220 Hom.: 6855

Bravo AF: 0.331

Asia WGS AF: 0.422 AC: 1465 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	4.7
Dann	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11098171; hg19: chr4-113710173;