6-30726039-A-G

Variant names:

• chr6-30726039-A-G
• rs3095329

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 0.26 in 152,136 control chromosomes in the GnomAD database, including 6,366 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 0.26 (6366 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.560
• Publications: 33 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.448 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: 0.260 AC: 39518 AN: 152018 Hom.: 6344 Cov.: 32

Gnomad AFR AF: 0.453

Gnomad AMI AF: 0.174

Gnomad AMR AF: 0.187

Gnomad ASJ AF: 0.186

Gnomad EAS AF: 0.175

Gnomad SAS AF: 0.153

Gnomad FIN AF: 0.102

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.202

Gnomad OTH AF: 0.265

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

GnomAD4 genome AF: 0.260 AC: 39574 AN: 152136 Hom.: 6366 Cov.: 32 AF XY: 0.250 AC XY: 18610 AN XY: 74402

African (AFR) AF: 0.453 AC: 18799 AN: 41462

American (AMR) AF: 0.187 AC: 2857 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.186 AC: 646 AN: 3464

East Asian (EAS) AF: 0.175 AC: 908 AN: 5186

South Asian (SAS) AF: 0.152 AC: 734 AN: 4828

European-Finnish (FIN) AF: 0.102 AC: 1086 AN: 10612

Middle Eastern (MID) AF: 0.279 AC: 82 AN: 294

European-Non Finnish (NFE) AF: 0.202 AC: 13739 AN: 67974

Other (OTH) AF: 0.267 AC: 564 AN: 2116

Alfa AF: 0.230 Hom.: 13402

Bravo AF: 0.276

Asia WGS AF: 0.223 AC: 776 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.2
DANN	Benign	0.45
PhyloP100		-0.56

Splicing

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

Other links and lift over

dbSNP: rs3095329; hg19: chr6-30693816;