rs676388

chr19-48708712-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.601-1301A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.464 in 151,950 control chromosomes in the GnomAD database, including 17,364 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 0.46 (17364 hom., cov: 32)
• Consequence: MAMSTR XM_047438640.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.86

Genes affected

MAMSTR (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.517 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MAMSTR	XM_047438640.1	c.601-1301A>G		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.464 AC: 70475 AN: 151832 Hom.: 17348 Cov.: 32

Gnomad AFR AF: 0.523

Gnomad AMI AF: 0.354

Gnomad AMR AF: 0.388

Gnomad ASJ AF: 0.475

Gnomad EAS AF: 0.00385

Gnomad SAS AF: 0.284

Gnomad FIN AF: 0.405

Gnomad MID AF: 0.596

Gnomad NFE AF: 0.502

Gnomad OTH AF: 0.481

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

GnomAD4 genome AF: 0.464 AC: 70526 AN: 151950 Hom.: 17364 Cov.: 32 AF XY: 0.451 AC XY: 33523 AN XY: 74266

Gnomad4 AFR AF: 0.523

Gnomad4 AMR AF: 0.387

Gnomad4 ASJ AF: 0.475

Gnomad4 EAS AF: 0.00386

Gnomad4 SAS AF: 0.284

Gnomad4 FIN AF: 0.405

Gnomad4 NFE AF: 0.502

Gnomad4 OTH AF: 0.478

Alfa AF: 0.473 Hom.: 9390

Bravo AF: 0.467

Asia WGS AF: 0.150 AC: 529 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	1.0
Dann	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs676388; hg19: chr19-49211969;