chr6-100094521-C-A

Variant names:

• chr6-100094521-C-A
• rs9484664
• ENST00000661108.2:n.373-12988C>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000661108.2(MCHR2-AS1):​n.373-12988C>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 ENST00000661108.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.162
• Publications: 1 publications found

Genes affected

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

ENSG00000295991 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000661108.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MCHR2-AS1	ENST00000661108.2		n.373-12988C>A		intron	N/A
	ENSG00000295991	ENST00000734864.1		n.48-29702C>A		intron	N/A
	MCHR2-AS1	ENST00000735332.1		n.264-4316C>A		intron	N/A

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

African (AFR) AF: 0.178 AC: 7276 AN: 40776

American (AMR) AF: 0.0944 AC: 1424 AN: 15092

Ashkenazi Jewish (ASJ) AF: 0.0802 AC: 277 AN: 3452

East Asian (EAS) AF: 0.000585 AC: 3 AN: 5130

South Asian (SAS) AF: 0.0175 AC: 83 AN: 4748

European-Finnish (FIN) AF: 0.0656 AC: 675 AN: 10288

Middle Eastern (MID) AF: 0.123 AC: 36 AN: 292

European-Non Finnish (NFE) AF: 0.108 AC: 7290 AN: 67696

Other (OTH) AF: 0.112 AC: 233 AN: 2078

Alfa AF: 0.114 Hom.: 142

Bravo AF: 0.121

Asia WGS AF: 0.0240 AC: 83 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	7.4
DANN	Benign	0.70
PhyloP100		-0.16

Splicing

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

Other links and lift over

dbSNP: rs9484664; hg19: chr6-100542397;