6-30135617-A-G

Variant names:

• chr6-30135617-A-G
• rs1541268

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 0.195 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
• Publications: 20 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.0936 AC: 3883 AN: 41504

American (AMR) AF: 0.202 AC: 3085 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.156 AC: 540 AN: 3460

East Asian (EAS) AF: 0.266 AC: 1375 AN: 5166

South Asian (SAS) AF: 0.219 AC: 1057 AN: 4826

European-Finnish (FIN) AF: 0.290 AC: 3064 AN: 10580

Middle Eastern (MID) AF: 0.0884 AC: 26 AN: 294

European-Non Finnish (NFE) AF: 0.235 AC: 15959 AN: 67974

Other (OTH) AF: 0.163 AC: 345 AN: 2112

Alfa AF: 0.214 Hom.: 9937

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
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs1541268; hg19: chr6-30103394;