rs7672287

chr4-3534275-A-C

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 0.221 in 151,902 control chromosomes in the GnomAD database, including 3,796 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 0.22 (3796 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.937

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.308 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: 0.221 AC: 33565 AN: 151784 Hom.: 3784 Cov.: 31

Gnomad AFR AF: 0.205

Gnomad AMI AF: 0.282

Gnomad AMR AF: 0.255

Gnomad ASJ AF: 0.190

Gnomad EAS AF: 0.170

Gnomad SAS AF: 0.324

Gnomad FIN AF: 0.199

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.225

Gnomad OTH AF: 0.208

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

GnomAD4 genome AF: 0.221 AC: 33608 AN: 151902 Hom.: 3796 Cov.: 31 AF XY: 0.223 AC XY: 16559 AN XY: 74230

Gnomad4 AFR AF: 0.205

Gnomad4 AMR AF: 0.256

Gnomad4 ASJ AF: 0.190

Gnomad4 EAS AF: 0.170

Gnomad4 SAS AF: 0.322

Gnomad4 FIN AF: 0.199

Gnomad4 NFE AF: 0.225

Gnomad4 OTH AF: 0.208

Alfa AF: 0.230 Hom.: 2509

Bravo AF: 0.221

Asia WGS AF: 0.248 AC: 861 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	3.2
Dann	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7672287; hg19: chr4-3536002;