6-30135617-A-G

Variant names:

• chr6-30135617-A-G
• rs1541268

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 0.195 in 152,112 control chromosomes in the GnomAD database, including 3,310 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 0.19 (3310 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.275

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.254 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: 0.195 AC: 29577 AN: 151994 Hom.: 3301 Cov.: 31

Gnomad AFR AF: 0.0934

Gnomad AMI AF: 0.305

Gnomad AMR AF: 0.201

Gnomad ASJ AF: 0.156

Gnomad EAS AF: 0.266

Gnomad SAS AF: 0.219

Gnomad FIN AF: 0.290

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.235

Gnomad OTH AF: 0.158

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

GnomAD4 genome AF: 0.195 AC: 29612 AN: 152112 Hom.: 3310 Cov.: 31 AF XY: 0.197 AC XY: 14676 AN XY: 74372

Gnomad4 AFR AF: 0.0936

Gnomad4 AMR AF: 0.202

Gnomad4 ASJ AF: 0.156

Gnomad4 EAS AF: 0.266

Gnomad4 SAS AF: 0.219

Gnomad4 FIN AF: 0.290

Gnomad4 NFE AF: 0.235

Gnomad4 OTH AF: 0.163

Alfa AF: 0.220 Hom.: 3131

Bravo AF: 0.181

Asia WGS AF: 0.259 AC: 900 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	3.4
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1541268; hg19: chr6-30103394;