rs10485092

Positions:

• chr6-84097959-T-G

Variant summary

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

The XM_017010221.3(MRAP2):​c.227+34967T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0521 in 152,244 control chromosomes in the GnomAD database, including 302 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 (302 hom., cov: 32)
• Consequence: MRAP2 XM_017010221.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.03

Genes affected

MRAP2 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0824 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MRAP2	XM_017010221.3	c.227+34967T>G		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0522 AC: 7935 AN: 152126 Hom.: 301 Cov.: 32

Gnomad AFR AF: 0.0144

Gnomad AMI AF: 0.134

Gnomad AMR AF: 0.0344

Gnomad ASJ AF: 0.0317

Gnomad EAS AF: 0.0397

Gnomad SAS AF: 0.0894

Gnomad FIN AF: 0.141

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0639

Gnomad OTH AF: 0.0445

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

GnomAD4 genome AF: 0.0521 AC: 7933 AN: 152244 Hom.: 302 Cov.: 32 AF XY: 0.0562 AC XY: 4184 AN XY: 74426

Gnomad4 AFR AF: 0.0143

Gnomad4 AMR AF: 0.0344

Gnomad4 ASJ AF: 0.0317

Gnomad4 EAS AF: 0.0398

Gnomad4 SAS AF: 0.0893

Gnomad4 FIN AF: 0.141

Gnomad4 NFE AF: 0.0639

Gnomad4 OTH AF: 0.0440

Alfa AF: 0.0607 Hom.: 157

Bravo AF: 0.0422

Asia WGS AF: 0.0640 AC: 222 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	2.8
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10485092; hg19: chr6-84807678;