rs41997

Variant names:

• chr7-118351841-A-G
• rs41997
• ENST00000433239.6:n.1178+27266A>G

Variant summary

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

The ENST00000433239.6(ANKRD7):​n.1178+27266A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.269 in 151,630 control chromosomes in the GnomAD database, including 6,179 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 0.27 (6179 hom., cov: 31)
• Consequence: ANKRD7 ENST00000433239.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.180
• Publications: 15 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]

LOC124901815 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.345 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ANKRD7	ENST00000433239.6	TSL:5	n.1178+27266A>G		intron	N/A
	ANKRD7	ENST00000634332.1	TSL:5	n.256+28845A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.269 AC: 40792 AN: 151512 Hom.: 6177 Cov.: 31

Gnomad AFR AF: 0.138

Gnomad AMI AF: 0.366

Gnomad AMR AF: 0.279

Gnomad ASJ AF: 0.413

Gnomad EAS AF: 0.286

Gnomad SAS AF: 0.192

Gnomad FIN AF: 0.220

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.348

Gnomad OTH AF: 0.315

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

GnomAD4 genome AF: 0.269 AC: 40793 AN: 151630 Hom.: 6179 Cov.: 31 AF XY: 0.262 AC XY: 19402 AN XY: 74110

African (AFR) AF: 0.138 AC: 5713 AN: 41444

American (AMR) AF: 0.279 AC: 4232 AN: 15174

Ashkenazi Jewish (ASJ) AF: 0.413 AC: 1431 AN: 3466

East Asian (EAS) AF: 0.286 AC: 1469 AN: 5128

South Asian (SAS) AF: 0.191 AC: 921 AN: 4816

European-Finnish (FIN) AF: 0.220 AC: 2328 AN: 10566

Middle Eastern (MID) AF: 0.378 AC: 111 AN: 294

European-Non Finnish (NFE) AF: 0.348 AC: 23594 AN: 67730

Other (OTH) AF: 0.314 AC: 660 AN: 2100

Alfa AF: 0.318 Hom.: 14573

Bravo AF: 0.273

Asia WGS AF: 0.229 AC: 800 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.8
DANN	Benign	0.47
PhyloP100		0.18

Splicing

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

Other links and lift over

dbSNP: rs41997; hg19: chr7-117991895;