chr7-53586664-G-C

Variant names:

• chr7-53586664-G-C
• rs2113757

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 0.881 in 152,260 control chromosomes in the GnomAD database, including 59,155 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 0.88 (59155 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.495

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.881 AC: 134027 AN: 152142 Hom.: 59108 Cov.: 33

Gnomad AFR AF: 0.875

Gnomad AMI AF: 0.673

Gnomad AMR AF: 0.899

Gnomad ASJ AF: 0.880

Gnomad EAS AF: 0.949

Gnomad SAS AF: 0.886

Gnomad FIN AF: 0.912

Gnomad MID AF: 0.854

Gnomad NFE AF: 0.873

Gnomad OTH AF: 0.879

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

GnomAD4 genome AF: 0.881 AC: 134132 AN: 152260 Hom.: 59155 Cov.: 33 AF XY: 0.884 AC XY: 65828 AN XY: 74448

Gnomad4 AFR AF: 0.875

Gnomad4 AMR AF: 0.899

Gnomad4 ASJ AF: 0.880

Gnomad4 EAS AF: 0.949

Gnomad4 SAS AF: 0.885

Gnomad4 FIN AF: 0.912

Gnomad4 NFE AF: 0.874

Gnomad4 OTH AF: 0.877

Alfa AF: 0.881 Hom.: 6910

Bravo AF: 0.878

Asia WGS AF: 0.887 AC: 3085 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.74
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2113757; hg19: chr7-53654357;