rs7673099

chr4-60321566-A-Cchr4-60321566-A-Gchr4-60321566-A-T

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 0.696 in 152,026 control chromosomes in the GnomAD database, including 38,933 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 0.70 (38933 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.121

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 (NFE) allele frequency at 95% confidence interval = 0.82 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.697 AC: 105832 AN: 151908 Hom.: 38936 Cov.: 33

Gnomad AFR AF: 0.455

Gnomad AMI AF: 0.784

Gnomad AMR AF: 0.765

Gnomad ASJ AF: 0.787

Gnomad EAS AF: 0.526

Gnomad SAS AF: 0.599

Gnomad FIN AF: 0.794

Gnomad MID AF: 0.845

Gnomad NFE AF: 0.825

Gnomad OTH AF: 0.724

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

GnomAD4 genome AF: 0.696 AC: 105849 AN: 152026 Hom.: 38933 Cov.: 33 AF XY: 0.693 AC XY: 51521 AN XY: 74320

Gnomad4 AFR AF: 0.455

Gnomad4 AMR AF: 0.765

Gnomad4 ASJ AF: 0.787

Gnomad4 EAS AF: 0.526

Gnomad4 SAS AF: 0.600

Gnomad4 FIN AF: 0.794

Gnomad4 NFE AF: 0.825

Gnomad4 OTH AF: 0.716

Alfa AF: 0.801 Hom.: 62995

Bravo AF: 0.687

Asia WGS AF: 0.515 AC: 1794 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	5.3
Dann	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7673099; hg19: chr4-61187284;