chr6-30792862-A-C

Variant names:

• chr6-30792862-A-C
• rs34682678

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.0240 AC: 998 AN: 41554

American (AMR) AF: 0.0805 AC: 1231 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0441 AC: 153 AN: 3470

East Asian (EAS) AF: 0.0552 AC: 286 AN: 5182

South Asian (SAS) AF: 0.0730 AC: 352 AN: 4824

European-Finnish (FIN) AF: 0.0702 AC: 744 AN: 10602

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.0796 AC: 5413 AN: 67996

Other (OTH) AF: 0.0581 AC: 123 AN: 2116

Alfa AF: 0.0700 Hom.: 204

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
PhyloP100		0.46

Splicing

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

Other links and lift over

dbSNP: rs34682678; hg19: chr6-30760639;