rs41997

chr7-118351841-A-G

Variant summary

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

The XR_007060646.1(LOC124901815):n.1517+27266A>G 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 0.269 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: LOC124901815 XR_007060646.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.180

Genes affected

LOC124901815 (HGNC:):

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=-0.9).
• 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/exons	MANE	UniProt
LOC124901815	XR_007060646.1	n.1517+27266A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ANKRD7	ENST00000433239.6	n.1178+27266A>G		intron_variant, non_coding_transcript_variant		5
ANKRD7	ENST00000634332.1	n.256+28845A>G		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.138

Gnomad4 AMR AF: 0.279

Gnomad4 ASJ AF: 0.413

Gnomad4 EAS AF: 0.286

Gnomad4 SAS AF: 0.191

Gnomad4 FIN AF: 0.220

Gnomad4 NFE AF: 0.348

Gnomad4 OTH AF: 0.314

Alfa AF: 0.319 Hom.: 2170

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs41997; hg19: chr7-117991895;