chr10-37219522-A-G

Variant summary

Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP7

The NM_052997.3(ANKRD30A):ā€‹c.3810A>Gā€‹(p.Ala1270Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: š‘“ 0.0 ( 0 hom., cov: 31)
Failed GnomAD Quality Control

Consequence

ANKRD30A
NM_052997.3 synonymous

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.650
Variant links:
Genes affected
ANKRD30A (HGNC:17234): (ankyrin repeat domain 30A) This gene encodes a DNA-binding transcription factor that is uniquely expressed in mammary epithelium and the testis. Altered expression levels have been associated with breast cancer progression. [provided by RefSeq, Nov 2016]

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -3 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.92).
BP7
Synonymous conserved (PhyloP=-0.65 with no splicing effect.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
ANKRD30ANM_052997.3 linkc.3810A>G p.Ala1270Ala synonymous_variant 34/36 ENST00000361713.2 NP_443723.3 Q9BXX3R4GNA2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
ANKRD30AENST00000361713.2 linkc.3810A>G p.Ala1270Ala synonymous_variant 34/365 NM_052997.3 ENSP00000354432.2 Q9BXX3R4GNA2
ANKRD30AENST00000374660.7 linkc.4167A>G p.Ala1389Ala synonymous_variant 40/425 ENSP00000363792.2 Q5W026
ANKRD30AENST00000602533.7 linkc.3810A>G p.Ala1270Ala synonymous_variant 34/365 ENSP00000473551.2 Q9BXX3
ANKRD30AENST00000696674.1 linkc.543A>G p.Ala181Ala synonymous_variant 1/2 ENSP00000512798.1 A0A8Q3WLF6

Frequencies

GnomAD3 genomes
AF:
0.00
AC:
0
AN:
150676
Hom.:
0
Cov.:
31
FAILED QC
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00
Gnomad OTH
AF:
0.00
GnomAD4 exome
Cov.:
67
GnomAD4 genome
Data not reliable, filtered out with message: AC0
AF:
0.00
AC:
0
AN:
150676
Hom.:
0
Cov.:
31
AF XY:
0.00
AC XY:
0
AN XY:
73552
Gnomad4 AFR
AF:
0.00
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.00
Gnomad4 OTH
AF:
0.00
EpiCase
AF:
0.0000546
EpiControl
AF:
0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.92
CADD
Benign
1.0
DANN
Benign
0.45

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: rs1148259; hg19: chr10-37508450; API