rs41943

Variant names:

• chr7-118320919-T-C
• rs41943
• ENST00000433239.6:n.906-1752T>C

Variant summary

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

The ENST00000433239.6(ANKRD7):​n.906-1752T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.639 in 152,072 control chromosomes in the GnomAD database, including 33,698 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 0.64 (33698 hom., cov: 32)
• Consequence: ANKRD7 ENST00000433239.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.31

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]

LOC102724495 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.07).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.894 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC102724495	XR_428238.2	n.56-1752T>C		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ANKRD7	ENST00000433239.6	n.906-1752T>C		intron_variant	Intron 8 of 15	5
ANKRD7	ENST00000634332.1	n.78-1752T>C		intron_variant	Intron 2 of 13	5

Frequencies

GnomAD3 genomes AF: 0.639 AC: 97085 AN: 151954 Hom.: 33633 Cov.: 32

Gnomad AFR AF: 0.901

Gnomad AMI AF: 0.442

Gnomad AMR AF: 0.694

Gnomad ASJ AF: 0.582

Gnomad EAS AF: 0.828

Gnomad SAS AF: 0.504

Gnomad FIN AF: 0.542

Gnomad MID AF: 0.627

Gnomad NFE AF: 0.482

Gnomad OTH AF: 0.648

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

GnomAD4 genome AF: 0.639 AC: 97203 AN: 152072 Hom.: 33698 Cov.: 32 AF XY: 0.641 AC XY: 47628 AN XY: 74312

Gnomad4 AFR AF: 0.902

Gnomad4 AMR AF: 0.695

Gnomad4 ASJ AF: 0.582

Gnomad4 EAS AF: 0.828

Gnomad4 SAS AF: 0.502

Gnomad4 FIN AF: 0.542

Gnomad4 NFE AF: 0.482

Gnomad4 OTH AF: 0.648

Alfa AF: 0.531 Hom.: 30736

Bravo AF: 0.669

Asia WGS AF: 0.681 AC: 2369 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.49
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs41943; hg19: chr7-117960973;