chr6-30097542-G-A

Variant names:

• chr6-30097542-G-A
• rs1264704

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 0.242 in 152,092 control chromosomes in the GnomAD database, including 5,261 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 0.24 (5261 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.230
• Publications: 18 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.395 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.242 AC: 36728 AN: 151974 Hom.: 5256 Cov.: 31

Gnomad AFR AF: 0.101

Gnomad AMI AF: 0.402

Gnomad AMR AF: 0.271

Gnomad ASJ AF: 0.334

Gnomad EAS AF: 0.410

Gnomad SAS AF: 0.237

Gnomad FIN AF: 0.349

Gnomad MID AF: 0.245

Gnomad NFE AF: 0.284

Gnomad OTH AF: 0.248

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

GnomAD4 genome AF: 0.242 AC: 36744 AN: 152092 Hom.: 5261 Cov.: 31 AF XY: 0.247 AC XY: 18391 AN XY: 74366

African (AFR) AF: 0.101 AC: 4193 AN: 41500

American (AMR) AF: 0.271 AC: 4141 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.334 AC: 1159 AN: 3472

East Asian (EAS) AF: 0.410 AC: 2116 AN: 5162

South Asian (SAS) AF: 0.236 AC: 1141 AN: 4830

European-Finnish (FIN) AF: 0.349 AC: 3680 AN: 10558

Middle Eastern (MID) AF: 0.250 AC: 73 AN: 292

European-Non Finnish (NFE) AF: 0.284 AC: 19338 AN: 67974

Other (OTH) AF: 0.254 AC: 537 AN: 2116

Alfa AF: 0.268 Hom.: 13393

Bravo AF: 0.231

Asia WGS AF: 0.309 AC: 1075 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.5
DANN	Benign	0.60
PhyloP100		-0.23

Splicing

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

Other links and lift over

dbSNP: rs1264704; hg19: chr6-30065319;