rs7672287

Variant names:

• chr4-3534275-A-C
• rs7672287

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;