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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC100420742		n.100093311A>G		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000275716	ENST00000612765.1	n.458T>C		splice_region_variant, non_coding_transcript_exon_variant	Exon 1 of 1	6
MCHR2-AS1	ENST00000661108.2	n.373-14198A>G		intron_variant	Intron 2 of 2
ENSG00000295991	ENST00000734864.1	n.48-30912A>G		intron_variant	Intron 1 of 3

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 v4.3

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;