11-103547140-T-C

Variant names:

• chr11-103547140-T-C
• rs716273

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 0.508 in 151,916 control chromosomes in the GnomAD database, including 20,079 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 0.51 (20079 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.639
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.566 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.508 AC: 77054 AN: 151798 Hom.: 20060 Cov.: 32

Gnomad AFR AF: 0.445

Gnomad AMI AF: 0.515

Gnomad AMR AF: 0.430

Gnomad ASJ AF: 0.583

Gnomad EAS AF: 0.268

Gnomad SAS AF: 0.438

Gnomad FIN AF: 0.574

Gnomad MID AF: 0.649

Gnomad NFE AF: 0.570

Gnomad OTH AF: 0.535

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

GnomAD4 genome AF: 0.508 AC: 77102 AN: 151916 Hom.: 20079 Cov.: 32 AF XY: 0.504 AC XY: 37405 AN XY: 74230

African (AFR) AF: 0.445 AC: 18455 AN: 41434

American (AMR) AF: 0.429 AC: 6555 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.583 AC: 2022 AN: 3466

East Asian (EAS) AF: 0.268 AC: 1379 AN: 5148

South Asian (SAS) AF: 0.438 AC: 2099 AN: 4796

European-Finnish (FIN) AF: 0.574 AC: 6056 AN: 10550

Middle Eastern (MID) AF: 0.643 AC: 189 AN: 294

European-Non Finnish (NFE) AF: 0.570 AC: 38753 AN: 67940

Other (OTH) AF: 0.534 AC: 1126 AN: 2108

Alfa AF: 0.550 Hom.: 72361

Bravo AF: 0.495

Asia WGS AF: 0.374 AC: 1301 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.82
DANN	Benign	0.68
PhyloP100		-0.64

Splicing

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

Other links and lift over

dbSNP: rs716273; hg19: chr11-103417868;