rs7671659

chr4-34351926-G-A

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 0.334 in 151,938 control chromosomes in the GnomAD database, including 12,840 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 0.33 (12840 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.965

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.706 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: 0.333 AC: 50612 AN: 151818 Hom.: 12790 Cov.: 32

Gnomad AFR AF: 0.713

Gnomad AMI AF: 0.0526

Gnomad AMR AF: 0.255

Gnomad ASJ AF: 0.222

Gnomad EAS AF: 0.134

Gnomad SAS AF: 0.353

Gnomad FIN AF: 0.189

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.168

Gnomad OTH AF: 0.290

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

GnomAD4 genome AF: 0.334 AC: 50726 AN: 151938 Hom.: 12840 Cov.: 32 AF XY: 0.333 AC XY: 24740 AN XY: 74246

Gnomad4 AFR AF: 0.713

Gnomad4 AMR AF: 0.255

Gnomad4 ASJ AF: 0.222

Gnomad4 EAS AF: 0.134

Gnomad4 SAS AF: 0.353

Gnomad4 FIN AF: 0.189

Gnomad4 NFE AF: 0.168

Gnomad4 OTH AF: 0.291

Alfa AF: 0.232 Hom.: 2465

Bravo AF: 0.351

Asia WGS AF: 0.315 AC: 1096 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
Cadd	Benign	0.061
Dann	Benign	0.18

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7671659; hg19: chr4-34353548;