10-37127448-T-C

Variant names:

• chr10-37127448-T-C
• rs1878249
• NM_052997.3:c.221+1440T>C

Variant summary

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

The NM_052997.3(ANKRD30A):​c.221+1440T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.488 in 151,858 control chromosomes in the GnomAD database, including 18,559 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 0.49 (18559 hom., cov: 31)
• Consequence: ANKRD30A NM_052997.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.05

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.746 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ANKRD30A	NM_052997.3	c.221+1440T>C		intron_variant	Intron 1 of 35	ENST00000361713.2	NP_443723.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ANKRD30A	ENST00000361713.2	c.221+1440T>C		intron_variant	Intron 1 of 35	5	NM_052997.3	ENSP00000354432.2
ANKRD30A	ENST00000374660.7	c.221+1440T>C		intron_variant	Intron 1 of 41	5		ENSP00000363792.2
ANKRD30A	ENST00000602533.7	c.221+1440T>C		intron_variant	Intron 1 of 35	5		ENSP00000473551.2

Frequencies

GnomAD3 genomes AF: 0.488 AC: 74091 AN: 151742 Hom.: 18549 Cov.: 31

Gnomad AFR AF: 0.512

Gnomad AMI AF: 0.438

Gnomad AMR AF: 0.487

Gnomad ASJ AF: 0.467

Gnomad EAS AF: 0.765

Gnomad SAS AF: 0.720

Gnomad FIN AF: 0.489

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.439

Gnomad OTH AF: 0.471

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

GnomAD4 genome AF: 0.488 AC: 74135 AN: 151858 Hom.: 18559 Cov.: 31 AF XY: 0.495 AC XY: 36693 AN XY: 74192

Gnomad4 AFR AF: 0.511

Gnomad4 AMR AF: 0.486

Gnomad4 ASJ AF: 0.467

Gnomad4 EAS AF: 0.766

Gnomad4 SAS AF: 0.720

Gnomad4 FIN AF: 0.489

Gnomad4 NFE AF: 0.439

Gnomad4 OTH AF: 0.475

Alfa AF: 0.451 Hom.: 18636

Bravo AF: 0.483

Asia WGS AF: 0.730 AC: 2520 AN: 3456

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.14
DANN	Benign	0.86

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: rs1878249; hg19: chr10-37416376;