rs4721923

Variant names:

• chr7-20598098-A-C
• rs4721923

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 0.387 in 151,946 control chromosomes in the GnomAD database, including 11,744 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 0.39 (11744 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0900

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 (EAS) allele frequency at 95% confidence interval = 0.59 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: 0.387 AC: 58721 AN: 151828 Hom.: 11726 Cov.: 31

Gnomad AFR AF: 0.384

Gnomad AMI AF: 0.530

Gnomad AMR AF: 0.491

Gnomad ASJ AF: 0.380

Gnomad EAS AF: 0.607

Gnomad SAS AF: 0.455

Gnomad FIN AF: 0.257

Gnomad MID AF: 0.379

Gnomad NFE AF: 0.361

Gnomad OTH AF: 0.422

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

GnomAD4 genome AF: 0.387 AC: 58774 AN: 151946 Hom.: 11744 Cov.: 31 AF XY: 0.389 AC XY: 28857 AN XY: 74254

Gnomad4 AFR AF: 0.384

Gnomad4 AMR AF: 0.492

Gnomad4 ASJ AF: 0.380

Gnomad4 EAS AF: 0.607

Gnomad4 SAS AF: 0.455

Gnomad4 FIN AF: 0.257

Gnomad4 NFE AF: 0.361

Gnomad4 OTH AF: 0.418

Alfa AF: 0.385 Hom.: 9011

Bravo AF: 0.406

Asia WGS AF: 0.495 AC: 1716 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.6
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4721923; hg19: chr7-20637721;