rs1611133

Variant names:

• chr6-29841605-C-T
• rs1611133

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 0.191 in 152,186 control chromosomes in the GnomAD database, including 2,979 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 (2979 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.318

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.229 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: 0.192 AC: 29124 AN: 152068 Hom.: 2980 Cov.: 32

Gnomad AFR AF: 0.147

Gnomad AMI AF: 0.190

Gnomad AMR AF: 0.162

Gnomad ASJ AF: 0.316

Gnomad EAS AF: 0.104

Gnomad SAS AF: 0.208

Gnomad FIN AF: 0.138

Gnomad MID AF: 0.245

Gnomad NFE AF: 0.232

Gnomad OTH AF: 0.190

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

GnomAD4 genome AF: 0.191 AC: 29140 AN: 152186 Hom.: 2979 Cov.: 32 AF XY: 0.188 AC XY: 13968 AN XY: 74414

Gnomad4 AFR AF: 0.148

Gnomad4 AMR AF: 0.162

Gnomad4 ASJ AF: 0.316

Gnomad4 EAS AF: 0.104

Gnomad4 SAS AF: 0.208

Gnomad4 FIN AF: 0.138

Gnomad4 NFE AF: 0.232

Gnomad4 OTH AF: 0.188

Alfa AF: 0.229 Hom.: 4426

Bravo AF: 0.190

Asia WGS AF: 0.139 AC: 486 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.69
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1611133; hg19: chr6-29809382;