rs11208994

chr1-67059360-A-Gchr1-67059360-A-T

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 0.318 in 151,612 control chromosomes in the GnomAD database, including 10,183 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 0.32 (10183 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.278

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.601 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.317 AC: 48061 AN: 151492 Hom.: 10147 Cov.: 31

Gnomad AFR AF: 0.606

Gnomad AMI AF: 0.321

Gnomad AMR AF: 0.264

Gnomad ASJ AF: 0.160

Gnomad EAS AF: 0.0966

Gnomad SAS AF: 0.193

Gnomad FIN AF: 0.168

Gnomad MID AF: 0.261

Gnomad NFE AF: 0.212

Gnomad OTH AF: 0.285

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

GnomAD4 genome AF: 0.318 AC: 48146 AN: 151612 Hom.: 10183 Cov.: 31 AF XY: 0.311 AC XY: 23039 AN XY: 74096

Gnomad4 AFR AF: 0.607

Gnomad4 AMR AF: 0.263

Gnomad4 ASJ AF: 0.160

Gnomad4 EAS AF: 0.0968

Gnomad4 SAS AF: 0.193

Gnomad4 FIN AF: 0.168

Gnomad4 NFE AF: 0.212

Gnomad4 OTH AF: 0.285

Alfa AF: 0.273 Hom.: 1677

Bravo AF: 0.336

Asia WGS AF: 0.192 AC: 671 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	1.4
Dann	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11208994; hg19: chr1-67525043;