7-10552033-T-C

Position:

• chr7-10552033-T-C

Variant summary

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

The NR_147499.1(MGC4859):​n.159+9449A>G 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 0.773 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 NR_147499.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.20

Genes affected

MGC4859 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
MGC4859	NR_147499.1	n.159+9449A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MGC4859	ENST00000634803.1	n.159+9449A>G		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.707

Gnomad4 AMR AF: 0.786

Gnomad4 ASJ AF: 0.758

Gnomad4 EAS AF: 0.506

Gnomad4 SAS AF: 0.726

Gnomad4 FIN AF: 0.840

Gnomad4 NFE AF: 0.824

Gnomad4 OTH AF: 0.764

Alfa AF: 0.781 Hom.: 7304

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10253058; hg19: chr7-10591660;