rs11208994

Variant names:

• chr1-67059360-A-G
• rs11208994

Your query was ambiguous. Multiple possible variants found:

• chr1-67059360-A-G
• chr1-67059360-A-T

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 0.318 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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.607 AC: 25061 AN: 41294

American (AMR) AF: 0.263 AC: 3999 AN: 15206

Ashkenazi Jewish (ASJ) AF: 0.160 AC: 554 AN: 3464

East Asian (EAS) AF: 0.0968 AC: 498 AN: 5144

South Asian (SAS) AF: 0.193 AC: 925 AN: 4802

European-Finnish (FIN) AF: 0.168 AC: 1770 AN: 10512

Middle Eastern (MID) AF: 0.260 AC: 76 AN: 292

European-Non Finnish (NFE) AF: 0.212 AC: 14372 AN: 67890

Other (OTH) AF: 0.285 AC: 598 AN: 2096

Alfa AF: 0.259 Hom.: 10237

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
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs11208994; hg19: chr1-67525043;