19-48711213-T-C

Variant summary

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

The XM_047438640.1(MAMSTR):c.600+2647A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.397 in 152,110 control chromosomes in the GnomAD database, including 12,753 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 0.40 (12753 hom., cov: 33)
• Consequence: MAMSTR XM_047438640.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.777

Genes affected

MAMSTR (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.826 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MAMSTR	XM_047438640.1	c.600+2647A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.396 AC: 60263 AN: 151992 Hom.: 12742 Cov.: 33

Gnomad AFR AF: 0.323

Gnomad AMI AF: 0.417

Gnomad AMR AF: 0.462

Gnomad ASJ AF: 0.448

Gnomad EAS AF: 0.847

Gnomad SAS AF: 0.431

Gnomad FIN AF: 0.449

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.379

Gnomad OTH AF: 0.394

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

GnomAD4 genome AF: 0.397 AC: 60324 AN: 152110 Hom.: 12753 Cov.: 33 AF XY: 0.403 AC XY: 29998 AN XY: 74374

Gnomad4 AFR AF: 0.323

Gnomad4 AMR AF: 0.462

Gnomad4 ASJ AF: 0.448

Gnomad4 EAS AF: 0.847

Gnomad4 SAS AF: 0.430

Gnomad4 FIN AF: 0.449

Gnomad4 NFE AF: 0.379

Gnomad4 OTH AF: 0.396

Alfa AF: 0.392 Hom.: 18091

Bravo AF: 0.397

Asia WGS AF: 0.642 AC: 2227 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	1.1
Dann	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs281380; hg19: chr19-49214470;