rs653403

Positions:

• chr11-124826395-T-A

Variant summary

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

The NR_103862.1(MSANTD2-AS1):​n.1307-6491T>A 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 0.709 in 152,070 control chromosomes in the GnomAD database, including 39,396 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 0.71 (39396 hom., cov: 31)
• Consequence: MSANTD2-AS1 NR_103862.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.645

Genes affected

MSANTD2-AS1 (HGNC:55601): (MSANTD2 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.867 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MSANTD2-AS1	NR_103862.1	n.1307-6491T>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MSANTD2-AS1	ENST00000499143.6	n.1285-6491T>A		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.709 AC: 107671 AN: 151952 Hom.: 39346 Cov.: 31

Gnomad AFR AF: 0.875

Gnomad AMI AF: 0.686

Gnomad AMR AF: 0.569

Gnomad ASJ AF: 0.752

Gnomad EAS AF: 0.440

Gnomad SAS AF: 0.624

Gnomad FIN AF: 0.600

Gnomad MID AF: 0.823

Gnomad NFE AF: 0.679

Gnomad OTH AF: 0.727

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

GnomAD4 genome AF: 0.709 AC: 107768 AN: 152070 Hom.: 39396 Cov.: 31 AF XY: 0.700 AC XY: 52015 AN XY: 74324

Gnomad4 AFR AF: 0.875

Gnomad4 AMR AF: 0.568

Gnomad4 ASJ AF: 0.752

Gnomad4 EAS AF: 0.439

Gnomad4 SAS AF: 0.625

Gnomad4 FIN AF: 0.600

Gnomad4 NFE AF: 0.679

Gnomad4 OTH AF: 0.731

Alfa AF: 0.690 Hom.: 4586

Bravo AF: 0.714

Asia WGS AF: 0.552 AC: 1924 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.76
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs653403; hg19: chr11-124696291;