NM_052997.3:c.221+1440T>C

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

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

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.511 AC: 21171 AN: 41414

American (AMR) AF: 0.486 AC: 7423 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.467 AC: 1622 AN: 3470

East Asian (EAS) AF: 0.766 AC: 3956 AN: 5166

South Asian (SAS) AF: 0.720 AC: 3465 AN: 4810

European-Finnish (FIN) AF: 0.489 AC: 5133 AN: 10502

Middle Eastern (MID) AF: 0.483 AC: 140 AN: 290

European-Non Finnish (NFE) AF: 0.439 AC: 29825 AN: 67930

Other (OTH) AF: 0.475 AC: 1001 AN: 2106

Alfa AF: 0.451 Hom.: 21692

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
PhyloP100		-1.1
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1878249; hg19: chr10-37416376;