7-10642782-A-T

Position:

• chr7-10642782-A-T

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

MGC4859 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
MGC4859	NR_147499.1	n.64-81205T>A		intron_variant
LOC107986766	XR_001745090.2	n.166+2273A>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MGC4859	ENST00000634803.1	n.64-81205T>A		intron_variant		1

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

Gnomad4 AFR AF: 0.540

Gnomad4 AMR AF: 0.439

Gnomad4 ASJ AF: 0.410

Gnomad4 EAS AF: 0.714

Gnomad4 SAS AF: 0.597

Gnomad4 FIN AF: 0.547

Gnomad4 NFE AF: 0.502

Gnomad4 OTH AF: 0.511

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
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

Publications

LitVar

Other links and lift over

dbSNP: rs2097903; hg19: chr7-10682409;