chr8-124606962-T-C

Position:

• chr8-124606962-T-C

Variant summary

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

The NM_014751.6(MTSS1):​c.209-15727A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.289 in 151,972 control chromosomes in the GnomAD database, including 7,818 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 0.29 (7818 hom., cov: 31)
• Consequence: MTSS1 NM_014751.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.40

Genes affected

MTSS1 (HGNC:20443): (MTSS I-BAR domain containing 1) Enables actin monomer binding activity; identical protein binding activity; and signaling receptor binding activity. Predicted to be involved in cellular response to fluid shear stress; negative regulation of epithelial cell proliferation; and urogenital system development. Predicted to act upstream of or within several processes, including actin filament polymerization; adherens junction maintenance; and magnesium ion homeostasis. Located in actin cytoskeleton. [provided by Alliance of Genome Resources, Apr 2022]

LOC124902016 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.487 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MTSS1	NM_014751.6	c.209-15727A>G		intron_variant		ENST00000518547.6	NP_055566.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MTSS1	ENST00000518547.6	c.209-15727A>G		intron_variant		1	NM_014751.6	ENSP00000429064.1

Frequencies

GnomAD3 genomes AF: 0.289 AC: 43877 AN: 151854 Hom.: 7794 Cov.: 31

Gnomad AFR AF: 0.492

Gnomad AMI AF: 0.323

Gnomad AMR AF: 0.288

Gnomad ASJ AF: 0.134

Gnomad EAS AF: 0.326

Gnomad SAS AF: 0.253

Gnomad FIN AF: 0.236

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.182

Gnomad OTH AF: 0.269

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

GnomAD4 genome AF: 0.289 AC: 43945 AN: 151972 Hom.: 7818 Cov.: 31 AF XY: 0.291 AC XY: 21650 AN XY: 74298

Gnomad4 AFR AF: 0.492

Gnomad4 AMR AF: 0.288

Gnomad4 ASJ AF: 0.134

Gnomad4 EAS AF: 0.326

Gnomad4 SAS AF: 0.252

Gnomad4 FIN AF: 0.236

Gnomad4 NFE AF: 0.182

Gnomad4 OTH AF: 0.274

Alfa AF: 0.193 Hom.: 6653

Bravo AF: 0.306

Asia WGS AF: 0.347 AC: 1205 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.26
DANN	Benign	0.45

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: rs2013845; hg19: chr8-125619203;