5-178698193-C-T

Variant names:

• chr5-178698193-C-T
• rs11743893
• ENST00000638723.1:n.*104-498G>A

Variant summary

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

The ENST00000638723.1(ENSG00000285978):​n.*104-498G>A variant causes a intron 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: ENSG00000285978 ENST00000638723.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.139
• Publications: 4 publications found

Genes affected

ENSG00000285978 (HGNC:):

MSANTD5 (HGNC:55184): (Myb/SANT DNA binding domain containing 5)

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
MSANTD5	XM_017010138.1	c.-104-498G>A		intron_variant	Intron 1 of 4		XP_016865627.1
MSANTD5	XR_007058568.1	n.535-498G>A		intron_variant	Intron 1 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000285978	ENST00000638723.1	n.*104-498G>A		intron_variant	Intron 4 of 7	5		ENSP00000492050.1

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

African (AFR) AF: 0.152 AC: 6301 AN: 41474

American (AMR) AF: 0.226 AC: 3454 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.231 AC: 802 AN: 3468

East Asian (EAS) AF: 0.331 AC: 1710 AN: 5162

South Asian (SAS) AF: 0.355 AC: 1711 AN: 4826

European-Finnish (FIN) AF: 0.371 AC: 3912 AN: 10546

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.255 AC: 17355 AN: 67984

Other (OTH) AF: 0.223 AC: 470 AN: 2112

Alfa AF: 0.237 Hom.: 2634

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
PhyloP100		-0.14
PromoterAI		-0.0012	Neutral

Splicing

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

Other links and lift over

dbSNP: rs11743893; hg19: chr5-178125194;