rs2746150

Variant names:

• chr6-29474924-C-T
• rs2746150
• ENST00000419416.1:n.*101G>A

Variant summary

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

The ENST00000419416.1(MAS1LP1):​n.*101G>A variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0521 in 152,296 control chromosomes in the GnomAD database, including 354 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 0.052 (354 hom., cov: 32)
  • Exomes 𝑓: 0.063 (0 hom.)
• Consequence: MAS1LP1 ENST00000419416.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.230

Genes affected

MAS1LP1 (HGNC:33448): (MAS1L pseudogene 1)

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 (NFE) allele frequency at 95% confidence interval = 0.091 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MAS1LP1	ENST00000419416.1	n.*101G>A		downstream_gene_variant		6

Frequencies

GnomAD3 genomes AF: 0.0522 AC: 7945 AN: 152162 Hom.: 354 Cov.: 32

Gnomad AFR AF: 0.0139

Gnomad AMI AF: 0.139

Gnomad AMR AF: 0.0220

Gnomad ASJ AF: 0.0196

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000207

Gnomad FIN AF: 0.0411

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.0930

Gnomad OTH AF: 0.0345

GnomAD4 exome AF: 0.0625 AC: 1 AN: 16 Hom.: 0 AF XY: 0.100 AC XY: 1 AN XY: 10

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.0521 AC: 7941 AN: 152280 Hom.: 354 Cov.: 32 AF XY: 0.0464 AC XY: 3458 AN XY: 74452

Gnomad4 AFR AF: 0.0139

Gnomad4 AMR AF: 0.0219

Gnomad4 ASJ AF: 0.0196

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000207

Gnomad4 FIN AF: 0.0411

Gnomad4 NFE AF: 0.0929

Gnomad4 OTH AF: 0.0341

Alfa AF: 0.0823 Hom.: 931

Bravo AF: 0.0496

Asia WGS AF: 0.00318 AC: 12 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	3.9
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2746150; hg19: chr6-29442701;