rs7796370

Variant names:

• chr7-92272402-C-A
• rs7796370
• NM_019004.2:c.-90-22487C>A

Your query was ambiguous. Multiple possible variants found:

• chr7-92272402-C-A
• chr7-92272402-C-G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 8 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_019004.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ANKIB1	NM_019004.2	MANE Select	c.-90-22487C>A		intron	N/A	NP_061877.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ANKIB1	ENST00000265742.8	TSL:1 MANE Select	c.-90-22487C>A		intron	N/A	ENSP00000265742.3

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

African (AFR) AF: 0.940 AC: 39082 AN: 41572

American (AMR) AF: 0.705 AC: 10761 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.846 AC: 2936 AN: 3470

East Asian (EAS) AF: 0.743 AC: 3839 AN: 5170

South Asian (SAS) AF: 0.781 AC: 3766 AN: 4822

European-Finnish (FIN) AF: 0.792 AC: 8383 AN: 10584

Middle Eastern (MID) AF: 0.735 AC: 216 AN: 294

European-Non Finnish (NFE) AF: 0.792 AC: 53872 AN: 67994

Other (OTH) AF: 0.814 AC: 1714 AN: 2106

Alfa AF: 0.804 Hom.: 208446

Bravo AF: 0.823

Asia WGS AF: 0.737 AC: 2567 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.88
DANN	Benign	0.58
PhyloP100		0.071
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: rs7796370; hg19: chr7-91901716;