rs7976914

chr12-65621787-C-Achr12-65621787-C-Gchr12-65621787-C-T

Variant summary

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

The NR_120431.1(MSRB3-AS1):n.334+20252G>T variant causes a intron, non coding transcript 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 NR_120431.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.845

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MSRB3-AS1	NR_120431.1	n.334+20252G>T		intron_variant, non_coding_transcript_variant
MSRB3-AS1	NR_120432.1	n.408+4825G>T		intron_variant, non_coding_transcript_variant
MSRB3-AS1	NR_120433.1	n.335-8510G>T		intron_variant, non_coding_transcript_variant
MSRB3-AS1	NR_120434.1	n.335-8510G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MSRB3-AS1	ENST00000537250.5	n.160+20252G>T		intron_variant, non_coding_transcript_variant		3

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

Gnomad4 AFR AF: 0.289

Gnomad4 AMR AF: 0.578

Gnomad4 ASJ AF: 0.775

Gnomad4 EAS AF: 0.709

Gnomad4 SAS AF: 0.654

Gnomad4 FIN AF: 0.807

Gnomad4 NFE AF: 0.750

Gnomad4 OTH AF: 0.665

Alfa AF: 0.734 Hom.: 81109

Bravo AF: 0.574

Asia WGS AF: 0.626 AC: 2173 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	5.6
Dann	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7976914; hg19: chr12-66015567;