rs4720913

Variant names:

• chr7-10836267-A-G
• rs4720913

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;