1-11304863-T-C

Variant names:

• chr1-11304863-T-C
• rs11121720

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 0.15 in 152,104 control chromosomes in the GnomAD database, including 3,659 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 0.15 (3659 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.15

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.54).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.396 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: 0.150 AC: 22797 AN: 151988 Hom.: 3636 Cov.: 32

Gnomad AFR AF: 0.401

Gnomad AMI AF: 0.00219

Gnomad AMR AF: 0.0713

Gnomad ASJ AF: 0.0686

Gnomad EAS AF: 0.119

Gnomad SAS AF: 0.145

Gnomad FIN AF: 0.0545

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0399

Gnomad OTH AF: 0.133

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

GnomAD4 genome AF: 0.150 AC: 22870 AN: 152104 Hom.: 3659 Cov.: 32 AF XY: 0.149 AC XY: 11096 AN XY: 74372

Gnomad4 AFR AF: 0.401

Gnomad4 AMR AF: 0.0711

Gnomad4 ASJ AF: 0.0686

Gnomad4 EAS AF: 0.119

Gnomad4 SAS AF: 0.145

Gnomad4 FIN AF: 0.0545

Gnomad4 NFE AF: 0.0399

Gnomad4 OTH AF: 0.132

Alfa AF: 0.0723 Hom.: 492

Bravo AF: 0.160

Asia WGS AF: 0.155 AC: 539 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.54
CADD	Benign	16
DANN	Benign	0.92

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11121720; hg19: chr1-11364920;