5-178698193-C-T

Variant summary

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

The XR_007058568.1(MSANTD5):n.535-498G>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 0.236 in 152,046 control chromosomes in the GnomAD database, including 4,523 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 0.24 (4523 hom., cov: 32)
• Consequence: MSANTD5 XR_007058568.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.139

Genes affected

MSANTD5 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.341 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MSANTD5	XR_007058568.1	n.535-498G>A		intron_variant, non_coding_transcript_variant
MSANTD5	XM_017010138.1	c.-104-498G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.236 AC: 35912 AN: 151928 Hom.: 4521 Cov.: 32

Gnomad AFR AF: 0.152

Gnomad AMI AF: 0.158

Gnomad AMR AF: 0.226

Gnomad ASJ AF: 0.231

Gnomad EAS AF: 0.331

Gnomad SAS AF: 0.354

Gnomad FIN AF: 0.371

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.255

Gnomad OTH AF: 0.216

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

GnomAD4 genome AF: 0.236 AC: 35932 AN: 152046 Hom.: 4523 Cov.: 32 AF XY: 0.244 AC XY: 18104 AN XY: 74332

Gnomad4 AFR AF: 0.152

Gnomad4 AMR AF: 0.226

Gnomad4 ASJ AF: 0.231

Gnomad4 EAS AF: 0.331

Gnomad4 SAS AF: 0.355

Gnomad4 FIN AF: 0.371

Gnomad4 NFE AF: 0.255

Gnomad4 OTH AF: 0.223

Alfa AF: 0.237 Hom.: 2399

Bravo AF: 0.218

Asia WGS AF: 0.354 AC: 1233 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	3.0
Dann	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11743893; hg19: chr5-178125194;