7-10552033-T-C

Variant names:

• chr7-10552033-T-C
• rs10253058
• ENST00000634803.1:n.159+9449A>G

Variant summary

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

The ENST00000634803.1(MGC4859):​n.159+9449A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.773 in 152,000 control chromosomes in the GnomAD database, including 45,785 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 0.77 (45785 hom., cov: 32)
• Consequence: MGC4859 ENST00000634803.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.20
• Publications: 0 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=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.818 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MGC4859	NR_147499.1	n.159+9449A>G		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MGC4859	ENST00000634803.1	n.159+9449A>G		intron_variant	Intron 2 of 2	1
MGC4859	ENST00000804835.1	n.96+9449A>G		intron_variant	Intron 1 of 1
MGC4859	ENST00000804836.1	n.96+9449A>G		intron_variant	Intron 1 of 2
MGC4859	ENST00000804847.1	n.96+9449A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.773 AC: 117382 AN: 151882 Hom.: 45747 Cov.: 32

Gnomad AFR AF: 0.707

Gnomad AMI AF: 0.746

Gnomad AMR AF: 0.786

Gnomad ASJ AF: 0.758

Gnomad EAS AF: 0.505

Gnomad SAS AF: 0.726

Gnomad FIN AF: 0.840

Gnomad MID AF: 0.797

Gnomad NFE AF: 0.824

Gnomad OTH AF: 0.767

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

GnomAD4 genome AF: 0.773 AC: 117472 AN: 152000 Hom.: 45785 Cov.: 32 AF XY: 0.772 AC XY: 57314 AN XY: 74274

African (AFR) AF: 0.707 AC: 29362 AN: 41506

American (AMR) AF: 0.786 AC: 11977 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.758 AC: 2629 AN: 3470

East Asian (EAS) AF: 0.506 AC: 2605 AN: 5148

South Asian (SAS) AF: 0.726 AC: 3497 AN: 4818

European-Finnish (FIN) AF: 0.840 AC: 8875 AN: 10562

Middle Eastern (MID) AF: 0.786 AC: 231 AN: 294

European-Non Finnish (NFE) AF: 0.824 AC: 56003 AN: 67948

Other (OTH) AF: 0.764 AC: 1613 AN: 2112

Alfa AF: 0.779 Hom.: 7509

Bravo AF: 0.765

Asia WGS AF: 0.642 AC: 2224 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.57
DANN	Benign	0.65
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs10253058; hg19: chr7-10591660;