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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124901815	XR_007060646.1	n.1517+27266A>G		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ANKRD7	ENST00000433239.6	n.1178+27266A>G		intron_variant	Intron 11 of 15	5
ANKRD7	ENST00000634332.1	n.256+28845A>G		intron_variant	Intron 4 of 13	5

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 v4.3

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;