ENST00000634803.1:n.64-81205T>A

Variant names:

• chr7-10642782-A-T
• rs2097903
• ENST00000634803.1:n.64-81205T>A

Variant summary

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

The ENST00000634803.1(MGC4859):​n.64-81205T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.517 in 151,806 control chromosomes in the GnomAD database, including 20,703 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 0.52 (20703 hom., cov: 31)
• Consequence: MGC4859 ENST00000634803.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0120
• Publications: 11 publications found

Genes affected

MGC4859 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.694 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MGC4859	NR_147499.1	n.64-81205T>A		intron_variant	Intron 1 of 2
LOC107986766	XR_001745090.2	n.166+2273A>T		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MGC4859	ENST00000634803.1	n.64-81205T>A		intron_variant	Intron 1 of 2	1
MGC4859	ENST00000804837.1	n.319-131T>A		intron_variant	Intron 3 of 3
MGC4859	ENST00000804838.1	n.187-131T>A		intron_variant	Intron 2 of 2
MGC4859	ENST00000804840.1	n.197+5566T>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.517 AC: 78463 AN: 151688 Hom.: 20678 Cov.: 31

Gnomad AFR AF: 0.539

Gnomad AMI AF: 0.552

Gnomad AMR AF: 0.439

Gnomad ASJ AF: 0.410

Gnomad EAS AF: 0.714

Gnomad SAS AF: 0.597

Gnomad FIN AF: 0.547

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.502

Gnomad OTH AF: 0.509

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

GnomAD4 genome AF: 0.517 AC: 78541 AN: 151806 Hom.: 20703 Cov.: 31 AF XY: 0.523 AC XY: 38785 AN XY: 74162

African (AFR) AF: 0.540 AC: 22319 AN: 41368

American (AMR) AF: 0.439 AC: 6691 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.410 AC: 1424 AN: 3472

East Asian (EAS) AF: 0.714 AC: 3670 AN: 5142

South Asian (SAS) AF: 0.597 AC: 2872 AN: 4810

European-Finnish (FIN) AF: 0.547 AC: 5762 AN: 10538

Middle Eastern (MID) AF: 0.537 AC: 158 AN: 294

European-Non Finnish (NFE) AF: 0.502 AC: 34065 AN: 67922

Other (OTH) AF: 0.511 AC: 1079 AN: 2112

Alfa AF: 0.516 Hom.: 2539

Bravo AF: 0.510

Asia WGS AF: 0.640 AC: 2228 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.8
DANN	Benign	0.74
PhyloP100		-0.012
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

Splicing

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

Other links and lift over

dbSNP: rs2097903; hg19: chr7-10682409;