rs10487393

Variant names:

• chr7-118237359-A-G
• rs10487393
• NM_019644.4:c.712+433A>G

Variant summary

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

The NM_019644.4(ANKRD7):​c.712+433A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0184 in 152,194 control chromosomes in the GnomAD database, including 43 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 0.018 (43 hom., cov: 32)
• Consequence: ANKRD7 NM_019644.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0730
• Publications: 1 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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0709 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_019644.4. 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
	ANKRD7	NM_019644.4	MANE Select	c.712+433A>G		intron	N/A	NP_062618.2	Q92527-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ANKRD7	ENST00000265224.9	TSL:1 MANE Select	c.712+433A>G		intron	N/A	ENSP00000265224.4	Q92527-1
	ANKRD7	ENST00000417525.5	TSL:5	c.712+433A>G		intron	N/A	ENSP00000395595.2	C9JIJ7
	ANKRD7	ENST00000477532.5	TSL:5	c.196+433A>G		intron	N/A	ENSP00000489121.1	A0A0U1RQQ7

Frequencies

GnomAD3 genomes AF: 0.0184 AC: 2799 AN: 152076 Hom.: 43 Cov.: 32

Gnomad AFR AF: 0.0189

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0417

Gnomad ASJ AF: 0.0199

Gnomad EAS AF: 0.0773

Gnomad SAS AF: 0.0286

Gnomad FIN AF: 0.00963

Gnomad MID AF: 0.0382

Gnomad NFE AF: 0.00909

Gnomad OTH AF: 0.0182

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

GnomAD4 genome AF: 0.0184 AC: 2801 AN: 152194 Hom.: 43 Cov.: 32 AF XY: 0.0198 AC XY: 1473 AN XY: 74398

African (AFR) AF: 0.0189 AC: 785 AN: 41532

American (AMR) AF: 0.0418 AC: 638 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.0199 AC: 69 AN: 3472

East Asian (EAS) AF: 0.0771 AC: 400 AN: 5186

South Asian (SAS) AF: 0.0289 AC: 139 AN: 4816

European-Finnish (FIN) AF: 0.00963 AC: 102 AN: 10592

Middle Eastern (MID) AF: 0.0411 AC: 12 AN: 292

European-Non Finnish (NFE) AF: 0.00906 AC: 616 AN: 68004

Other (OTH) AF: 0.0190 AC: 40 AN: 2110

Alfa AF: 0.0126 Hom.: 5

Bravo AF: 0.0226

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.1
DANN	Benign	0.67
PhyloP100		-0.073
Mutation Taster		=100/0	polymorphism

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: rs10487393; hg19: chr7-117877413;