rs10487391

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_019644.4(ANKRD7):​c.144G>A​(p.Lys48Lys) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0152 in 1,614,048 control chromosomes in the GnomAD database, including 509 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 0.018 ( 44 hom., cov: 31)
Exomes 𝑓: 0.015 ( 465 hom. )

Consequence

ANKRD7
NM_019644.4 synonymous

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.38
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.83).
BP7
Synonymous conserved (PhyloP=1.38 with no splicing effect.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0709 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
ANKRD7NM_019644.4 linkuse as main transcriptc.144G>A p.Lys48Lys synonymous_variant 1/7 ENST00000265224.9 NP_062618.2 Q92527-1A0A140VJE5

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
ANKRD7ENST00000265224.9 linkuse as main transcriptc.144G>A p.Lys48Lys synonymous_variant 1/71 NM_019644.4 ENSP00000265224.4 Q92527-1

Frequencies

GnomAD3 genomes
AF:
0.0184
AC:
2793
AN:
152156
Hom.:
44
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.0188
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0415
Gnomad ASJ
AF:
0.0199
Gnomad EAS
AF:
0.0773
Gnomad SAS
AF:
0.0286
Gnomad FIN
AF:
0.00951
Gnomad MID
AF:
0.0380
Gnomad NFE
AF:
0.00913
Gnomad OTH
AF:
0.0182
GnomAD3 exomes
AF:
0.0293
AC:
7239
AN:
247188
Hom.:
291
AF XY:
0.0255
AC XY:
3432
AN XY:
134354
show subpopulations
Gnomad AFR exome
AF:
0.0191
Gnomad AMR exome
AF:
0.0931
Gnomad ASJ exome
AF:
0.0228
Gnomad EAS exome
AF:
0.0815
Gnomad SAS exome
AF:
0.0251
Gnomad FIN exome
AF:
0.00728
Gnomad NFE exome
AF:
0.00877
Gnomad OTH exome
AF:
0.0240
GnomAD4 exome
AF:
0.0149
AC:
21708
AN:
1461774
Hom.:
465
Cov.:
33
AF XY:
0.0148
AC XY:
10736
AN XY:
727194
show subpopulations
Gnomad4 AFR exome
AF:
0.0198
Gnomad4 AMR exome
AF:
0.0828
Gnomad4 ASJ exome
AF:
0.0214
Gnomad4 EAS exome
AF:
0.0775
Gnomad4 SAS exome
AF:
0.0250
Gnomad4 FIN exome
AF:
0.00638
Gnomad4 NFE exome
AF:
0.00904
Gnomad4 OTH exome
AF:
0.0161
GnomAD4 genome
AF:
0.0183
AC:
2793
AN:
152274
Hom.:
44
Cov.:
31
AF XY:
0.0198
AC XY:
1472
AN XY:
74468
show subpopulations
Gnomad4 AFR
AF:
0.0187
Gnomad4 AMR
AF:
0.0416
Gnomad4 ASJ
AF:
0.0199
Gnomad4 EAS
AF:
0.0771
Gnomad4 SAS
AF:
0.0288
Gnomad4 FIN
AF:
0.00951
Gnomad4 NFE
AF:
0.00910
Gnomad4 OTH
AF:
0.0189
Alfa
AF:
0.00504
Hom.:
25
Bravo
AF:
0.0227
EpiCase
AF:
0.0115
EpiControl
AF:
0.0106

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.83
CADD
Benign
2.4
DANN
Benign
0.43

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs10487391; hg19: chr7-117865028; COSMIC: COSV54554948; API