rs2057684

Positions:

• chr7-118251118-A-C

Variant summary

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

The ENST00000433239.6(ANKRD7):​n.756-8719A>C variant causes a intron, non coding transcript 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.213

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ANKRD7	ENST00000433239.6	n.756-8719A>C		intron_variant, non_coding_transcript_variant		5
ANKRD7	ENST00000634332.1	n.25-8719A>C		intron_variant, non_coding_transcript_variant		5

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

Gnomad4 AFR AF: 0.0641

Gnomad4 AMR AF: 0.0479

Gnomad4 ASJ AF: 0.0199

Gnomad4 EAS AF: 0.0772

Gnomad4 SAS AF: 0.0284

Gnomad4 FIN AF: 0.00960

Gnomad4 NFE AF: 0.00918

Gnomad4 OTH AF: 0.0304

Alfa AF: 0.0204 Hom.: 18

Bravo AF: 0.0373

Asia WGS AF: 0.0530 AC: 184 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2057684; hg19: chr7-117891172;