rs4721923

Variant names:

• chr7-20598098-A-C
• rs4721923

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.384 AC: 15909 AN: 41400

American (AMR) AF: 0.492 AC: 7513 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.380 AC: 1319 AN: 3470

East Asian (EAS) AF: 0.607 AC: 3138 AN: 5166

South Asian (SAS) AF: 0.455 AC: 2191 AN: 4820

European-Finnish (FIN) AF: 0.257 AC: 2708 AN: 10556

Middle Eastern (MID) AF: 0.373 AC: 109 AN: 292

European-Non Finnish (NFE) AF: 0.361 AC: 24523 AN: 67938

Other (OTH) AF: 0.418 AC: 882 AN: 2110

Alfa AF: 0.380 Hom.: 28319

Bravo AF: 0.406

Asia WGS AF: 0.495 AC: 1716 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.6
DANN	Benign	0.54
PhyloP100		-0.090

Splicing

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

Other links and lift over

dbSNP: rs4721923; hg19: chr7-20637721;