rs985937

Variant names:

• chr6-100093311-A-G
• rs985937
• ENST00000612765.1:n.458T>C

Your query was ambiguous. Multiple possible variants found:

• chr6-100093311-A-G
• chr6-100093311-A-T

Variant summary

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

The ENST00000612765.1(ENSG00000275716):​n.458T>C variant causes a splice region, non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.651 in 342,420 control chromosomes in the GnomAD database, including 73,869 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 0.66 (33928 hom., cov: 30)
  • Exomes 𝑓: 0.64 (39941 hom.)
• Consequence: ENSG00000275716 ENST00000612765.1 splice_region, non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0510
• Publications: 1 publications found

Genes affected

ENSG00000275716 (HGNC:):

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.748 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000612765.1. 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
	ENSG00000275716	ENST00000612765.1	TSL:6	n.458T>C		splice_region non_coding_transcript_exon	Exon 1 of 1
	MCHR2-AS1	ENST00000661108.2		n.373-14198A>G		intron	N/A
	ENSG00000295991	ENST00000734864.1		n.48-30912A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.664 AC: 100733 AN: 151680 Hom.: 33881 Cov.: 30

Gnomad AFR AF: 0.755

Gnomad AMI AF: 0.584

Gnomad AMR AF: 0.648

Gnomad ASJ AF: 0.587

Gnomad EAS AF: 0.742

Gnomad SAS AF: 0.750

Gnomad FIN AF: 0.628

Gnomad MID AF: 0.728

Gnomad NFE AF: 0.611

Gnomad OTH AF: 0.658

GnomAD4 exome AF: 0.641 AC: 122224 AN: 190622 Hom.: 39941 Cov.: 0 AF XY: 0.652 AC XY: 71973 AN XY: 110326

African (AFR) AF: 0.749 AC: 2210 AN: 2952

American (AMR) AF: 0.609 AC: 6907 AN: 11340

Ashkenazi Jewish (ASJ) AF: 0.556 AC: 2338 AN: 4204

East Asian (EAS) AF: 0.743 AC: 2331 AN: 3138

South Asian (SAS) AF: 0.732 AC: 27093 AN: 37012

European-Finnish (FIN) AF: 0.630 AC: 10834 AN: 17210

Middle Eastern (MID) AF: 0.645 AC: 453 AN: 702

European-Non Finnish (NFE) AF: 0.612 AC: 64153 AN: 104822

Other (OTH) AF: 0.639 AC: 5905 AN: 9242

GnomAD4 genome AF: 0.664 AC: 100832 AN: 151798 Hom.: 33928 Cov.: 30 AF XY: 0.669 AC XY: 49617 AN XY: 74188

African (AFR) AF: 0.755 AC: 31268 AN: 41398

American (AMR) AF: 0.649 AC: 9895 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.587 AC: 2033 AN: 3466

East Asian (EAS) AF: 0.741 AC: 3799 AN: 5124

South Asian (SAS) AF: 0.750 AC: 3585 AN: 4782

European-Finnish (FIN) AF: 0.628 AC: 6632 AN: 10556

Middle Eastern (MID) AF: 0.738 AC: 217 AN: 294

European-Non Finnish (NFE) AF: 0.611 AC: 41491 AN: 67914

Other (OTH) AF: 0.659 AC: 1379 AN: 2094

Alfa AF: 0.652 Hom.: 7425

Bravo AF: 0.667

Asia WGS AF: 0.773 AC: 2687 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	4.2
DANN	Benign	0.29
PhyloP100		-0.051

Splicing

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

Other links and lift over

dbSNP: rs985937; hg19: chr6-100541187;