rs653403

Variant names:

• chr11-124826395-T-A
• rs653403
• ENST00000499143.6:n.1285-6491T>A

Variant summary

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

The ENST00000499143.6(MSANTD2-AS1):​n.1285-6491T>A variant causes a intron 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 ENST00000499143.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.645
• Publications: 2 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
MSANTD2-AS1	NR_103862.1	n.1307-6491T>A		intron_variant	Intron 4 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MSANTD2-AS1	ENST00000499143.6	n.1285-6491T>A		intron_variant	Intron 4 of 4	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

African (AFR) AF: 0.875 AC: 36318 AN: 41512

American (AMR) AF: 0.568 AC: 8670 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.752 AC: 2611 AN: 3472

East Asian (EAS) AF: 0.439 AC: 2265 AN: 5154

South Asian (SAS) AF: 0.625 AC: 3004 AN: 4810

European-Finnish (FIN) AF: 0.600 AC: 6352 AN: 10584

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

European-Non Finnish (NFE) AF: 0.679 AC: 46143 AN: 67966

Other (OTH) AF: 0.731 AC: 1538 AN: 2104

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
PhyloP100		-0.65

Splicing

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

Other links and lift over

dbSNP: rs653403; hg19: chr11-124696291;