chr1-11553106-C-T

Variant names:

• chr1-11553106-C-T
• rs2817611

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 0.219 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
• Publications: 6 publications found

ACMG classification

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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.571 AC: 23623 AN: 41384

American (AMR) AF: 0.104 AC: 1595 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.127 AC: 441 AN: 3468

East Asian (EAS) AF: 0.0841 AC: 435 AN: 5174

South Asian (SAS) AF: 0.233 AC: 1119 AN: 4810

European-Finnish (FIN) AF: 0.108 AC: 1135 AN: 10558

Middle Eastern (MID) AF: 0.195 AC: 57 AN: 292

European-Non Finnish (NFE) AF: 0.0666 AC: 4526 AN: 67986

Other (OTH) AF: 0.178 AC: 376 AN: 2110

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
PhyloP100		2.2

Splicing

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

Other links and lift over

dbSNP: rs2817611; hg19: chr1-11613163;