rs4720913

Positions:

• chr7-10836267-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 0.511 in 151,954 control chromosomes in the GnomAD database, including 20,475 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 0.51 (20475 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.328

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.61 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.511 AC: 77528 AN: 151836 Hom.: 20439 Cov.: 32

Gnomad AFR AF: 0.616

Gnomad AMI AF: 0.625

Gnomad AMR AF: 0.576

Gnomad ASJ AF: 0.607

Gnomad EAS AF: 0.491

Gnomad SAS AF: 0.479

Gnomad FIN AF: 0.320

Gnomad MID AF: 0.557

Gnomad NFE AF: 0.458

Gnomad OTH AF: 0.535

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

GnomAD4 genome AF: 0.511 AC: 77617 AN: 151954 Hom.: 20475 Cov.: 32 AF XY: 0.507 AC XY: 37666 AN XY: 74258

Gnomad4 AFR AF: 0.617

Gnomad4 AMR AF: 0.577

Gnomad4 ASJ AF: 0.607

Gnomad4 EAS AF: 0.491

Gnomad4 SAS AF: 0.479

Gnomad4 FIN AF: 0.320

Gnomad4 NFE AF: 0.458

Gnomad4 OTH AF: 0.534

Alfa AF: 0.469 Hom.: 29351

Bravo AF: 0.537

Asia WGS AF: 0.478 AC: 1667 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.0
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4720913; hg19: chr7-10875894;