15-79449251-T-G

Variant names:

• chr15-79449251-T-G
• rs7169963
• NM_015206.3:c.-50-6847T>G

Variant summary

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

The NM_015206.3(MINAR1):​c.-50-6847T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.307 in 152,088 control chromosomes in the GnomAD database, including 8,528 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 0.31 (8528 hom., cov: 32)
• Consequence: MINAR1 NM_015206.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.52

Genes affected

MINAR1 (HGNC:29172): (membrane integral NOTCH2 associated receptor 1) Involved in several processes, including negative regulation of TOR signaling; negative regulation of angiogenesis; and negative regulation of protein ubiquitination. Located in plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.516 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MINAR1	NM_015206.3	c.-50-6847T>G		intron_variant	Intron 1 of 3	ENST00000305428.8	NP_056021.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MINAR1	ENST00000305428.8	c.-50-6847T>G		intron_variant	Intron 1 of 3	1	NM_015206.3	ENSP00000307461.3

Frequencies

GnomAD3 genomes AF: 0.306 AC: 46513 AN: 151970 Hom.: 8486 Cov.: 32

Gnomad AFR AF: 0.521

Gnomad AMI AF: 0.171

Gnomad AMR AF: 0.241

Gnomad ASJ AF: 0.208

Gnomad EAS AF: 0.271

Gnomad SAS AF: 0.237

Gnomad FIN AF: 0.179

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.225

Gnomad OTH AF: 0.298

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

GnomAD4 genome AF: 0.307 AC: 46620 AN: 152088 Hom.: 8528 Cov.: 32 AF XY: 0.303 AC XY: 22514 AN XY: 74374

Gnomad4 AFR AF: 0.522

Gnomad4 AMR AF: 0.241

Gnomad4 ASJ AF: 0.208

Gnomad4 EAS AF: 0.271

Gnomad4 SAS AF: 0.236

Gnomad4 FIN AF: 0.179

Gnomad4 NFE AF: 0.225

Gnomad4 OTH AF: 0.302

Alfa AF: 0.229 Hom.: 8561

Bravo AF: 0.320

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.24
DANN	Benign	0.49

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: rs7169963; hg19: chr15-79741593;