rs34682678

chr6-30792862-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 0.0613 in 152,242 control chromosomes in the GnomAD database, including 335 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 0.061 (335 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.464

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0778 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: 0.0614 AC: 9343 AN: 152124 Hom.: 336 Cov.: 32

Gnomad AFR AF: 0.0240

Gnomad AMI AF: 0.00877

Gnomad AMR AF: 0.0805

Gnomad ASJ AF: 0.0441

Gnomad EAS AF: 0.0556

Gnomad SAS AF: 0.0733

Gnomad FIN AF: 0.0702

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.0796

Gnomad OTH AF: 0.0583

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

GnomAD4 genome AF: 0.0613 AC: 9340 AN: 152242 Hom.: 335 Cov.: 32 AF XY: 0.0619 AC XY: 4610 AN XY: 74438

Gnomad4 AFR AF: 0.0240

Gnomad4 AMR AF: 0.0805

Gnomad4 ASJ AF: 0.0441

Gnomad4 EAS AF: 0.0552

Gnomad4 SAS AF: 0.0730

Gnomad4 FIN AF: 0.0702

Gnomad4 NFE AF: 0.0796

Gnomad4 OTH AF: 0.0581

Alfa AF: 0.0830 Hom.: 198

Bravo AF: 0.0600

Asia WGS AF: 0.0750 AC: 262 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	6.6
Dann	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs34682678; hg19: chr6-30760639;