chr1-11553106-C-T

Position:

• chr1-11553106-C-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 0.219 in 151,976 control chromosomes in the GnomAD database, including 7,294 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 0.22 (7294 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.24

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.565 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: 0.219 AC: 33309 AN: 151856 Hom.: 7277 Cov.: 31

Gnomad AFR AF: 0.571

Gnomad AMI AF: 0.0559

Gnomad AMR AF: 0.105

Gnomad ASJ AF: 0.127

Gnomad EAS AF: 0.0843

Gnomad SAS AF: 0.232

Gnomad FIN AF: 0.108

Gnomad MID AF: 0.197

Gnomad NFE AF: 0.0666

Gnomad OTH AF: 0.182

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

GnomAD4 genome AF: 0.219 AC: 33358 AN: 151976 Hom.: 7294 Cov.: 31 AF XY: 0.219 AC XY: 16273 AN XY: 74310

Gnomad4 AFR AF: 0.571

Gnomad4 AMR AF: 0.104

Gnomad4 ASJ AF: 0.127

Gnomad4 EAS AF: 0.0841

Gnomad4 SAS AF: 0.233

Gnomad4 FIN AF: 0.108

Gnomad4 NFE AF: 0.0666

Gnomad4 OTH AF: 0.178

Alfa AF: 0.156 Hom.: 567

Bravo AF: 0.229

Asia WGS AF: 0.189 AC: 656 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	13
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2817611; hg19: chr1-11613163;