rs9484664

Variant names:

• chr6-100094521-C-A
• rs9484664
• ENST00000661108.1:n.345-12988C>A

Variant summary

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

The ENST00000661108.1(MCHR2-AS1):​n.345-12988C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.115 in 150,464 control chromosomes in the GnomAD database, including 1,160 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 0.12 (1160 hom., cov: 31)
• Consequence: MCHR2-AS1 ENST00000661108.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.162

Genes affected

MCHR2-AS1 (HGNC:48980): (MCHR2 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.175 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
MCHR2-AS1	ENST00000661108.1	n.345-12988C>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.115 AC: 17339 AN: 150350 Hom.: 1159 Cov.: 31

Gnomad AFR AF: 0.178

Gnomad AMI AF: 0.0636

Gnomad AMR AF: 0.0945

Gnomad ASJ AF: 0.0802

Gnomad EAS AF: 0.000583

Gnomad SAS AF: 0.0175

Gnomad FIN AF: 0.0656

Gnomad MID AF: 0.128

Gnomad NFE AF: 0.108

Gnomad OTH AF: 0.113

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

GnomAD4 genome AF: 0.115 AC: 17355 AN: 150464 Hom.: 1160 Cov.: 31 AF XY: 0.111 AC XY: 8186 AN XY: 73464

Gnomad4 AFR AF: 0.178

Gnomad4 AMR AF: 0.0944

Gnomad4 ASJ AF: 0.0802

Gnomad4 EAS AF: 0.000585

Gnomad4 SAS AF: 0.0175

Gnomad4 FIN AF: 0.0656

Gnomad4 NFE AF: 0.108

Gnomad4 OTH AF: 0.112

Alfa AF: 0.111 Hom.: 130

Bravo AF: 0.121

Asia WGS AF: 0.0240 AC: 83 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	7.4
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9484664; hg19: chr6-100542397;