rs1667599

Variant names:

• chr2-74174647-G-A
• rs1667599
• NM_018221.5:c.15-1895C>T

Your query was ambiguous. Multiple possible variants found:

• chr2-74174647-G-A
• chr2-74174647-G-C

Variant summary

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

The NM_018221.5(MOB1A):​c.15-1895C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.892 in 152,240 control chromosomes in the GnomAD database, including 60,939 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 0.89 (60939 hom., cov: 32)
• Consequence: MOB1A NM_018221.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.800
• Publications: 1 publications found

Genes affected

MOB1A (HGNC:16015): (MOB kinase activator 1A) The protein encoded by this gene is a component of the Hippo signaling pathway, which controls organ size and tumor growth by enhancing apoptosis. Loss of the encoded protein results in cell proliferation and cancer formation. The encoded protein is also involved in the control of microtubule stability during cytokinesis. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Nov 2015]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MOB1A	NM_018221.5	c.15-1895C>T		intron_variant	Intron 1 of 5	ENST00000396049.5	NP_060691.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MOB1A	ENST00000396049.5	c.15-1895C>T		intron_variant	Intron 1 of 5	1	NM_018221.5	ENSP00000379364.3

Frequencies

GnomAD3 genomes AF: 0.892 AC: 135696 AN: 152122 Hom.: 60871 Cov.: 32

Gnomad AFR AF: 0.972

Gnomad AMI AF: 0.834

Gnomad AMR AF: 0.903

Gnomad ASJ AF: 0.904

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.969

Gnomad FIN AF: 0.825

Gnomad MID AF: 0.908

Gnomad NFE AF: 0.838

Gnomad OTH AF: 0.897

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

GnomAD4 genome AF: 0.892 AC: 135822 AN: 152240 Hom.: 60939 Cov.: 32 AF XY: 0.894 AC XY: 66490 AN XY: 74412

African (AFR) AF: 0.972 AC: 40388 AN: 41562

American (AMR) AF: 0.903 AC: 13794 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.904 AC: 3138 AN: 3472

East Asian (EAS) AF: 1.00 AC: 5184 AN: 5186

South Asian (SAS) AF: 0.970 AC: 4679 AN: 4826

European-Finnish (FIN) AF: 0.825 AC: 8727 AN: 10582

Middle Eastern (MID) AF: 0.912 AC: 268 AN: 294

European-Non Finnish (NFE) AF: 0.838 AC: 56982 AN: 68012

Other (OTH) AF: 0.898 AC: 1901 AN: 2116

Alfa AF: 0.858 Hom.: 19287

Bravo AF: 0.902

Asia WGS AF: 0.984 AC: 3417 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.6
DANN	Benign	0.80
PhyloP100		0.80
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: rs1667599; hg19: chr2-74401774;