rs7976914

Variant names:

• chr12-65621787-C-A
• rs7976914
• ENST00000535315.5:n.193+4825G>T

Your query was ambiguous. Multiple possible variants found:

• chr12-65621787-C-A
• chr12-65621787-C-G
• chr12-65621787-C-T

Variant summary

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

The ENST00000535315.5(MSRB3-AS1):​n.193+4825G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.607 in 152,014 control chromosomes in the GnomAD database, including 31,250 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 0.61 (31250 hom., cov: 32)
• Consequence: MSRB3-AS1 ENST00000535315.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.845
• Publications: 6 publications found

Genes affected

MSRB3-AS1 (HGNC:53386): (MSRB3 antisense RNA 1)

LINC02454 (HGNC:53387): (long intergenic non-protein coding RNA 2454)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.745 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000535315.5. 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
	MSRB3-AS1	NR_120431.1		n.334+20252G>T		intron	N/A
	MSRB3-AS1	NR_120432.1		n.408+4825G>T		intron	N/A
	MSRB3-AS1	NR_120433.1		n.335-8510G>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MSRB3-AS1	ENST00000535315.5	TSL:3	n.193+4825G>T		intron	N/A
	MSRB3-AS1	ENST00000537250.5	TSL:3	n.160+20252G>T		intron	N/A
	MSRB3-AS1	ENST00000537298.5	TSL:3	n.123-8510G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.607 AC: 92249 AN: 151896 Hom.: 31245 Cov.: 32

Gnomad AFR AF: 0.289

Gnomad AMI AF: 0.857

Gnomad AMR AF: 0.579

Gnomad ASJ AF: 0.775

Gnomad EAS AF: 0.708

Gnomad SAS AF: 0.654

Gnomad FIN AF: 0.807

Gnomad MID AF: 0.816

Gnomad NFE AF: 0.750

Gnomad OTH AF: 0.664

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

GnomAD4 genome AF: 0.607 AC: 92273 AN: 152014 Hom.: 31250 Cov.: 32 AF XY: 0.611 AC XY: 45407 AN XY: 74306

African (AFR) AF: 0.289 AC: 11978 AN: 41412

American (AMR) AF: 0.578 AC: 8818 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.775 AC: 2687 AN: 3468

East Asian (EAS) AF: 0.709 AC: 3656 AN: 5160

South Asian (SAS) AF: 0.654 AC: 3154 AN: 4822

European-Finnish (FIN) AF: 0.807 AC: 8547 AN: 10594

Middle Eastern (MID) AF: 0.820 AC: 241 AN: 294

European-Non Finnish (NFE) AF: 0.750 AC: 51009 AN: 67984

Other (OTH) AF: 0.665 AC: 1401 AN: 2106

Alfa AF: 0.702 Hom.: 121155

Bravo AF: 0.574

Asia WGS AF: 0.626 AC: 2173 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	5.6
DANN	Benign	0.57
PhyloP100		0.84

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs7976914;

hg19: chr12-66015567;