chr7-127492511-C-G

Position:

• chr7-127492511-C-G

Variant summary

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

The variant allele was found at a frequency of 0.699 in 152,050 control chromosomes in the GnomAD database, including 37,489 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 0.70 (37489 hom., cov: 33)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.923

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.927 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.127492511C>G		intergenic_region
LOC105375490	XR_001745351.2	n.2793-7229G>C		intron_variant
LOC105375490	XR_001745352.2	n.995-7229G>C		intron_variant
LOC105375490	XR_007060511.1	n.676-7229G>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.699 AC: 106162 AN: 151934 Hom.: 37452 Cov.: 33

Gnomad AFR AF: 0.680

Gnomad AMI AF: 0.727

Gnomad AMR AF: 0.647

Gnomad ASJ AF: 0.632

Gnomad EAS AF: 0.949

Gnomad SAS AF: 0.713

Gnomad FIN AF: 0.800

Gnomad MID AF: 0.642

Gnomad NFE AF: 0.689

Gnomad OTH AF: 0.692

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

GnomAD4 genome AF: 0.699 AC: 106244 AN: 152050 Hom.: 37489 Cov.: 33 AF XY: 0.706 AC XY: 52499 AN XY: 74326

Gnomad4 AFR AF: 0.680

Gnomad4 AMR AF: 0.647

Gnomad4 ASJ AF: 0.632

Gnomad4 EAS AF: 0.949

Gnomad4 SAS AF: 0.713

Gnomad4 FIN AF: 0.800

Gnomad4 NFE AF: 0.689

Gnomad4 OTH AF: 0.688

Alfa AF: 0.699 Hom.: 4656

Bravo AF: 0.684

Asia WGS AF: 0.792 AC: 2742 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.29
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1018852; hg19: chr7-127132565;