rs7796370

chr7-92272402-C-Achr7-92272402-C-G

Variant summary

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

The NM_019004.2(ANKIB1):c.-90-22487C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.822 in 152,184 control chromosomes in the GnomAD database, including 52,004 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 0.82 (52004 hom., cov: 31)
• Consequence: ANKIB1 NM_019004.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0710

Genes affected

ANKIB1 (HGNC:22215): (ankyrin repeat and IBR domain containing 1) Predicted to enable ubiquitin conjugating enzyme binding activity and ubiquitin protein ligase activity. Predicted to be involved in positive regulation of proteasomal ubiquitin-dependent protein catabolic process; protein polyubiquitination; and ubiquitin-dependent protein catabolic process. Predicted to be part of ubiquitin ligase complex. Predicted to be active in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.932 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ANKIB1	NM_019004.2	c.-90-22487C>A		intron_variant		ENST00000265742.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ANKIB1	ENST00000265742.8	c.-90-22487C>A		intron_variant		1	NM_019004.2	P1

Frequencies

GnomAD3 genomes AF: 0.822 AC: 125028 AN: 152066 Hom.: 51942 Cov.: 31

Gnomad AFR AF: 0.940

Gnomad AMI AF: 0.632

Gnomad AMR AF: 0.706

Gnomad ASJ AF: 0.846

Gnomad EAS AF: 0.741

Gnomad SAS AF: 0.779

Gnomad FIN AF: 0.792

Gnomad MID AF: 0.731

Gnomad NFE AF: 0.792

Gnomad OTH AF: 0.815

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

GnomAD4 genome AF: 0.822 AC: 125145 AN: 152184 Hom.: 52004 Cov.: 31 AF XY: 0.820 AC XY: 60975 AN XY: 74402

Gnomad4 AFR AF: 0.940

Gnomad4 AMR AF: 0.705

Gnomad4 ASJ AF: 0.846

Gnomad4 EAS AF: 0.743

Gnomad4 SAS AF: 0.781

Gnomad4 FIN AF: 0.792

Gnomad4 NFE AF: 0.792

Gnomad4 OTH AF: 0.814

Alfa AF: 0.800 Hom.: 96589

Bravo AF: 0.823

Asia WGS AF: 0.737 AC: 2567 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	0.88
Dann	Benign	0.58

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

Publications

LitVar

Other links and lift over

dbSNP: rs7796370; hg19: chr7-91901716;