rs7169803

Variant names:

• chr15-40279915-G-A
• rs7169803
• NM_001190479.3:c.*1529C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001190479.3(ANKRD63):​c.*1529C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.662 in 152,146 control chromosomes in the GnomAD database, including 34,670 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 0.66 (34670 hom., cov: 34)
• Consequence: ANKRD63 NM_001190479.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.83
• Publications: 2 publications found

Genes affected

ANKRD63 (HGNC:40027): (ankyrin repeat domain 63)

PLCB2 (HGNC:9055): (phospholipase C beta 2) The protein encoded by this gene is a phosphodiesterase that catalyzes the hydrolysis of phosphatidylinositol 4,5-bisphosphate to the second messengers inositol 1,4,5-trisphosphate (IP3) and diacylglycerol. The encoded protein is activated by G proteins and has been shown to be involved in the type 2 taste receptor signal transduction pathway. In addition, nuclear factor kappa B can regulate the transcription of this gene, whose protein product is also an important regulator of platelet responses. [provided by RefSeq, Jan 2017]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.744 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ANKRD63	NM_001190479.3	c.*1529C>T		3_prime_UTR_variant	Exon 1 of 1	ENST00000434396.2	NP_001177408.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ANKRD63	ENST00000434396.2	c.*1529C>T		3_prime_UTR_variant	Exon 1 of 1	6	NM_001190479.3	ENSP00000399547.1
PLCB2	ENST00000560009.1	n.395-1571C>T		intron_variant	Intron 2 of 2	4

Frequencies

GnomAD3 genomes AF: 0.662 AC: 100674 AN: 152030 Hom.: 34655 Cov.: 34

Gnomad AFR AF: 0.512

Gnomad AMI AF: 0.781

Gnomad AMR AF: 0.743

Gnomad ASJ AF: 0.783

Gnomad EAS AF: 0.323

Gnomad SAS AF: 0.764

Gnomad FIN AF: 0.680

Gnomad MID AF: 0.777

Gnomad NFE AF: 0.743

Gnomad OTH AF: 0.686

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

GnomAD4 genome AF: 0.662 AC: 100730 AN: 152146 Hom.: 34670 Cov.: 34 AF XY: 0.661 AC XY: 49151 AN XY: 74394

African (AFR) AF: 0.511 AC: 21224 AN: 41508

American (AMR) AF: 0.743 AC: 11371 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.783 AC: 2714 AN: 3468

East Asian (EAS) AF: 0.323 AC: 1670 AN: 5172

South Asian (SAS) AF: 0.764 AC: 3689 AN: 4828

European-Finnish (FIN) AF: 0.680 AC: 7213 AN: 10604

Middle Eastern (MID) AF: 0.767 AC: 224 AN: 292

European-Non Finnish (NFE) AF: 0.743 AC: 50459 AN: 67954

Other (OTH) AF: 0.690 AC: 1455 AN: 2110

Alfa AF: 0.716 Hom.: 90143

Bravo AF: 0.656

Asia WGS AF: 0.587 AC: 2044 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.021
DANN	Benign	0.81
PhyloP100		-3.8

Splicing

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

Other links and lift over

dbSNP: rs7169803; hg19: chr15-40572116; COSMIC: COSV53047060;