rs3757797

Positions:

• chr7-118231984-A-C

Variant summary

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

The NM_019644.4(ANKRD7):​c.180-2447A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0321 in 152,204 control chromosomes in the GnomAD database, including 129 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 0.032 (129 hom., cov: 32)
• Consequence: ANKRD7 NM_019644.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.348

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0715 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ANKRD7	NM_019644.4	c.180-2447A>C		intron_variant		ENST00000265224.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ANKRD7	ENST00000265224.9	c.180-2447A>C		intron_variant		1	NM_019644.4	P2

Frequencies

GnomAD3 genomes AF: 0.0321 AC: 4879 AN: 152086 Hom.: 127 Cov.: 32

Gnomad AFR AF: 0.0660

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0478

Gnomad ASJ AF: 0.0199

Gnomad EAS AF: 0.0779

Gnomad SAS AF: 0.0288

Gnomad FIN AF: 0.00960

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.00919

Gnomad OTH AF: 0.0297

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

GnomAD4 genome AF: 0.0321 AC: 4887 AN: 152204 Hom.: 129 Cov.: 32 AF XY: 0.0328 AC XY: 2439 AN XY: 74442

Gnomad4 AFR AF: 0.0660

Gnomad4 AMR AF: 0.0479

Gnomad4 ASJ AF: 0.0199

Gnomad4 EAS AF: 0.0777

Gnomad4 SAS AF: 0.0288

Gnomad4 FIN AF: 0.00960

Gnomad4 NFE AF: 0.00916

Gnomad4 OTH AF: 0.0303

Alfa AF: 0.0206 Hom.: 12

Bravo AF: 0.0380

Asia WGS AF: 0.0540 AC: 187 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	8.4
DANN	Benign	0.88

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

Publications

LitVar

Other links and lift over

dbSNP: rs3757797; hg19: chr7-117872038;