rs2057684

Variant names:

• chr7-118251118-A-C
• rs2057684
• ENST00000433239.6:n.756-8719A>C

Variant summary

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

The ENST00000433239.6(ANKRD7):​n.756-8719A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0316 in 152,176 control chromosomes in the GnomAD database, including 124 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 0.032 (124 hom., cov: 32)
• Consequence: ANKRD7 ENST00000433239.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.213
• Publications: 3 publications found

Genes affected

ANKRD7 (HGNC:18588): (ankyrin repeat domain 7) Predicted to act upstream of or within blastocyst hatching. Located in centrosome and nucleoplasm. [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=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.071 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000433239.6. 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
	ANKRD7	ENST00000433239.6	TSL:5	n.756-8719A>C		intron	N/A
	ANKRD7	ENST00000634332.1	TSL:5	n.25-8719A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0315 AC: 4795 AN: 152058 Hom.: 122 Cov.: 32

Gnomad AFR AF: 0.0641

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0478

Gnomad ASJ AF: 0.0199

Gnomad EAS AF: 0.0774

Gnomad SAS AF: 0.0283

Gnomad FIN AF: 0.00960

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.00921

Gnomad OTH AF: 0.0297

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

GnomAD4 genome AF: 0.0316 AC: 4803 AN: 152176 Hom.: 124 Cov.: 32 AF XY: 0.0324 AC XY: 2408 AN XY: 74404

African (AFR) AF: 0.0641 AC: 2663 AN: 41542

American (AMR) AF: 0.0479 AC: 731 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.0199 AC: 69 AN: 3466

East Asian (EAS) AF: 0.0772 AC: 400 AN: 5180

South Asian (SAS) AF: 0.0284 AC: 137 AN: 4830

European-Finnish (FIN) AF: 0.00960 AC: 102 AN: 10620

Middle Eastern (MID) AF: 0.0442 AC: 13 AN: 294

European-Non Finnish (NFE) AF: 0.00918 AC: 624 AN: 67952

Other (OTH) AF: 0.0304 AC: 64 AN: 2108

Alfa AF: 0.0232 Hom.: 21

Bravo AF: 0.0373

Asia WGS AF: 0.0530 AC: 184 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.8
DANN	Benign	0.63
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs2057684; hg19: chr7-117891172;