7-99824373-A-G

Variant names:

• chr7-99824373-A-G
• rs620020

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 0.238 in 152,128 control chromosomes in the GnomAD database, including 9,596 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 0.24 (9596 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.792
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.653 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.238 AC: 36129 AN: 152010 Hom.: 9563 Cov.: 32

Gnomad AFR AF: 0.659

Gnomad AMI AF: 0.134

Gnomad AMR AF: 0.144

Gnomad ASJ AF: 0.0879

Gnomad EAS AF: 0.00250

Gnomad SAS AF: 0.0769

Gnomad FIN AF: 0.0581

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.0700

Gnomad OTH AF: 0.205

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

GnomAD4 genome AF: 0.238 AC: 36217 AN: 152128 Hom.: 9596 Cov.: 32 AF XY: 0.231 AC XY: 17213 AN XY: 74388

African (AFR) AF: 0.660 AC: 27357 AN: 41472

American (AMR) AF: 0.144 AC: 2198 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0879 AC: 305 AN: 3470

East Asian (EAS) AF: 0.00251 AC: 13 AN: 5180

South Asian (SAS) AF: 0.0772 AC: 372 AN: 4820

European-Finnish (FIN) AF: 0.0581 AC: 616 AN: 10600

Middle Eastern (MID) AF: 0.136 AC: 40 AN: 294

European-Non Finnish (NFE) AF: 0.0701 AC: 4763 AN: 67986

Other (OTH) AF: 0.204 AC: 431 AN: 2110

Alfa AF: 0.155 Hom.: 599

Bravo AF: 0.263

Asia WGS AF: 0.0750 AC: 263 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.6
DANN	Benign	0.33
PhyloP100		-0.79

Splicing

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

Other links and lift over

dbSNP: rs620020; hg19: chr7-99421996;