rs1611133

Variant names:

• chr6-29841605-C-T
• rs1611133

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 0.191 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
• Publications: 31 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.148 AC: 6131 AN: 41512

American (AMR) AF: 0.162 AC: 2472 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.316 AC: 1095 AN: 3468

East Asian (EAS) AF: 0.104 AC: 541 AN: 5188

South Asian (SAS) AF: 0.208 AC: 1004 AN: 4824

European-Finnish (FIN) AF: 0.138 AC: 1464 AN: 10588

Middle Eastern (MID) AF: 0.240 AC: 70 AN: 292

European-Non Finnish (NFE) AF: 0.232 AC: 15793 AN: 67998

Other (OTH) AF: 0.188 AC: 397 AN: 2112

Alfa AF: 0.220 Hom.: 6827

Bravo AF: 0.190

Asia WGS AF: 0.139 AC: 486 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.69
DANN	Benign	0.73
PhyloP100		-0.32

Splicing

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

Other links and lift over

dbSNP: rs1611133; hg19: chr6-29809382;