rs11207272

chr1-58607758-T-Cchr1-58607758-T-G

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 0.205 in 152,154 control chromosomes in the GnomAD database, including 4,625 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 0.20 (4625 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.299

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.421 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: 0.205 AC: 31131 AN: 152036 Hom.: 4614 Cov.: 32

Gnomad AFR AF: 0.426

Gnomad AMI AF: 0.150

Gnomad AMR AF: 0.125

Gnomad ASJ AF: 0.141

Gnomad EAS AF: 0.203

Gnomad SAS AF: 0.162

Gnomad FIN AF: 0.0548

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.119

Gnomad OTH AF: 0.187

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

GnomAD4 genome AF: 0.205 AC: 31166 AN: 152154 Hom.: 4625 Cov.: 32 AF XY: 0.199 AC XY: 14772 AN XY: 74396

Gnomad4 AFR AF: 0.426

Gnomad4 AMR AF: 0.125

Gnomad4 ASJ AF: 0.141

Gnomad4 EAS AF: 0.202

Gnomad4 SAS AF: 0.162

Gnomad4 FIN AF: 0.0548

Gnomad4 NFE AF: 0.119

Gnomad4 OTH AF: 0.184

Alfa AF: 0.134 Hom.: 2255

Bravo AF: 0.220

Asia WGS AF: 0.200 AC: 695 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	4.2
Dann	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11207272; hg19: chr1-59073430; COSMIC: COSV59945699;