rs734674

Variant names:

• chr6-279695-C-G
• rs734674

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 0.0788 in 150,482 control chromosomes in the GnomAD database, including 124 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 0.079 (124 hom., cov: 44)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0110

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 = 0.0881 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: 0.0788 AC: 11854 AN: 150372 Hom.: 124 Cov.: 44

Gnomad AFR AF: 0.0638

Gnomad AMI AF: 0.104

Gnomad AMR AF: 0.0546

Gnomad ASJ AF: 0.110

Gnomad EAS AF: 0.0637

Gnomad SAS AF: 0.0776

Gnomad FIN AF: 0.0967

Gnomad MID AF: 0.0637

Gnomad NFE AF: 0.0900

Gnomad OTH AF: 0.0794

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

GnomAD4 genome AF: 0.0788 AC: 11860 AN: 150482 Hom.: 124 Cov.: 44 AF XY: 0.0780 AC XY: 5735 AN XY: 73558

Gnomad4 AFR AF: 0.0637

Gnomad4 AMR AF: 0.0546

Gnomad4 ASJ AF: 0.110

Gnomad4 EAS AF: 0.0635

Gnomad4 SAS AF: 0.0773

Gnomad4 FIN AF: 0.0967

Gnomad4 NFE AF: 0.0900

Gnomad4 OTH AF: 0.0819

Alfa AF: 0.0780 Hom.: 21

Asia WGS AF: 0.0860 AC: 297 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	6.6
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs734674; hg19: chr6-279695;