rs4510766

chr7-107852344-A-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 0.364 in 152,174 control chromosomes in the GnomAD database, including 11,407 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 0.36 (11407 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.383

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.512 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.364 AC: 55418 AN: 152056 Hom.: 11401 Cov.: 32

Gnomad AFR AF: 0.166

Gnomad AMI AF: 0.513

Gnomad AMR AF: 0.398

Gnomad ASJ AF: 0.466

Gnomad EAS AF: 0.529

Gnomad SAS AF: 0.320

Gnomad FIN AF: 0.456

Gnomad MID AF: 0.341

Gnomad NFE AF: 0.447

Gnomad OTH AF: 0.383

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

GnomAD4 genome AF: 0.364 AC: 55423 AN: 152174 Hom.: 11407 Cov.: 32 AF XY: 0.366 AC XY: 27220 AN XY: 74390

Gnomad4 AFR AF: 0.166

Gnomad4 AMR AF: 0.398

Gnomad4 ASJ AF: 0.466

Gnomad4 EAS AF: 0.529

Gnomad4 SAS AF: 0.320

Gnomad4 FIN AF: 0.456

Gnomad4 NFE AF: 0.447

Gnomad4 OTH AF: 0.380

Alfa AF: 0.434 Hom.: 11026

Bravo AF: 0.355

Asia WGS AF: 0.413 AC: 1435 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	5.6
Dann	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4510766; hg19: chr7-107492789;