ENST00000433239.6:n.906-1752T>C

Variant names:

• chr7-118320919-T-C
• rs41943
• ENST00000433239.6:n.906-1752T>C

Variant summary

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

The ENST00000433239.6(ANKRD7):​n.906-1752T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.639 in 152,072 control chromosomes in the GnomAD database, including 33,698 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 0.64 (33698 hom., cov: 32)
• Consequence: ANKRD7 ENST00000433239.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.31
• Publications: 6 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]

LOC102724495 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.07).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.894 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.906-1752T>C		intron	N/A
	ANKRD7	ENST00000634332.1	TSL:5	n.78-1752T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.639 AC: 97085 AN: 151954 Hom.: 33633 Cov.: 32

Gnomad AFR AF: 0.901

Gnomad AMI AF: 0.442

Gnomad AMR AF: 0.694

Gnomad ASJ AF: 0.582

Gnomad EAS AF: 0.828

Gnomad SAS AF: 0.504

Gnomad FIN AF: 0.542

Gnomad MID AF: 0.627

Gnomad NFE AF: 0.482

Gnomad OTH AF: 0.648

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

GnomAD4 genome AF: 0.639 AC: 97203 AN: 152072 Hom.: 33698 Cov.: 32 AF XY: 0.641 AC XY: 47628 AN XY: 74312

African (AFR) AF: 0.902 AC: 37435 AN: 41514

American (AMR) AF: 0.695 AC: 10602 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.582 AC: 2019 AN: 3472

East Asian (EAS) AF: 0.828 AC: 4274 AN: 5160

South Asian (SAS) AF: 0.502 AC: 2418 AN: 4818

European-Finnish (FIN) AF: 0.542 AC: 5725 AN: 10558

Middle Eastern (MID) AF: 0.622 AC: 183 AN: 294

European-Non Finnish (NFE) AF: 0.482 AC: 32777 AN: 67976

Other (OTH) AF: 0.648 AC: 1367 AN: 2110

Alfa AF: 0.538 Hom.: 41230

Bravo AF: 0.669

Asia WGS AF: 0.681 AC: 2369 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.49
DANN	Benign	0.39
PhyloP100		-2.3

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs41943;

hg19: chr7-117960973;