rs281379

chr19-48711017-G-A

Variant summary

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

The XM_047438640.1(MAMSTR):c.600+2843C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.377 in 152,018 control chromosomes in the GnomAD database, including 12,250 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 0.38 (12250 hom., cov: 32)
• Consequence: MAMSTR XM_047438640.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.411

Genes affected

MAMSTR (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.488 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MAMSTR	XM_047438640.1	c.600+2843C>T		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.377 AC: 57336 AN: 151900 Hom.: 12251 Cov.: 32

Gnomad AFR AF: 0.240

Gnomad AMI AF: 0.358

Gnomad AMR AF: 0.349

Gnomad ASJ AF: 0.478

Gnomad EAS AF: 0.00346

Gnomad SAS AF: 0.266

Gnomad FIN AF: 0.404

Gnomad MID AF: 0.582

Gnomad NFE AF: 0.493

Gnomad OTH AF: 0.414

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

GnomAD4 genome AF: 0.377 AC: 57356 AN: 152018 Hom.: 12250 Cov.: 32 AF XY: 0.368 AC XY: 27350 AN XY: 74306

Gnomad4 AFR AF: 0.241

Gnomad4 AMR AF: 0.348

Gnomad4 ASJ AF: 0.478

Gnomad4 EAS AF: 0.00347

Gnomad4 SAS AF: 0.265

Gnomad4 FIN AF: 0.404

Gnomad4 NFE AF: 0.493

Gnomad4 OTH AF: 0.411

Alfa AF: 0.448 Hom.: 20605

Bravo AF: 0.368

Asia WGS AF: 0.139 AC: 489 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	0.87
Dann	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs281379; hg19: chr19-49214274;